Mon Feb 15 16:52:17 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped
/airflow/apps/freesurfer/bin/recon-all
-all -i DICOM/I0 -s stripped
subjid stripped
setenv SUBJECTS_DIR /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Actual FREESURFER_HOME /airflow/apps/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux mercury-224.braincode.ca 4.4.0-173-generic #203-Ubuntu SMP Wed Jan 15 02:55:01 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc      96269 
maxlocks     unlimited
maxsignal    96269 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:       24688512     1927448      997512      213152    21763552    22319580
Swap:       3906556      520064     3386492

########################################
program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/02/15-21:52:17-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:18-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:18-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:18-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:18-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

ProgramName: mri_robust_register.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:18-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

ProgramName: mri_robust_template  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:18-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:18-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:18-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:18-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:18-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/02/15-21:52:18-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $  User: airflow  Machine: mercury-224.braincode.ca  Platform: Linux  PlatformVersion: 4.4.0-173-generic  CompilerName: GCC  CompilerVersion: 40400 
#######################################
GCADIR /airflow/apps/freesurfer/average
GCA RB_all_2016-05-10.vc700.gca
GCASkull RB_all_withskull_2016-05-10.vc700.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /airflow/apps/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped

 mri_convert /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/DICOM/I0 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/orig/001.mgz 

mri_convert.bin /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/DICOM/I0 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/DICOM/I0...
Getting Series No 
INFO: Found 779 files in /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/DICOM
INFO: Scanning for Series Number 13
Scanning Directory 
INFO: found 176 files in series
INFO: loading series header info.

RunNo = 12
INFO: sorting.
sdfiSameSlicePos() eps = 0.000001
INFO: (256 256 176), nframes = 1, ismosaic=0
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
PE Dir ROW ROW
AutoAlign matrix detected 
AutoAlign Matrix --------------------- 
 1.00000   0.00000   0.00000   0.00000;
 0.00000   1.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;

FileName 		/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/DICOM/I0
Identification
	NumarisVer        syngo MR E11
	ScannerModel      Prisma_fit
	PatientName       TUTORIAL
Date and time
	StudyDate         20000101
	StudyTime         180730.226000 
	SeriesTime        181839.972000 
	AcqTime           181134.945000 
Acquisition parameters
	PulseSeq          tfl3d4_16ns 
	Protocol          T1w_MPR_vNav_4e 
	PhEncDir          ROW
	EchoNo            1
	FlipAngle         7
	EchoTime          1.69
	InversionTime     1250
	RepetitionTime    2530
	PhEncFOV          256
	ReadoutFOV        256
Image information
	RunNo             12
	SeriesNo          13
	ImageNo           1
	NImageRows        256
	NImageCols        256
	NFrames           1
	SliceArraylSize   1
	IsMosaic          0
	ImgPos             93.1993 139.6246 133.7124 
	VolRes              1.0000   1.0000   1.0000 
	VolDim            256      256      176 
	Vc                  0.0398  -0.9922  -0.1184 
	Vr                 -0.0644   0.1157  -0.9912 
	Vs                 -0.9971  -0.0471   0.0593 
	VolCenter           2.2979  23.2904  -3.0915 
	TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 0
INFO: no Siemens slice order reversal detected (good!). 
TR=2530.00, TE=1.69, TI=1250.00, flip angle=7.00
i_ras = (0.039788, -0.992172, -0.118368)
j_ras = (-0.0644291, 0.115668, -0.991196)
k_ras = (-0.997129, -0.047064, 0.0593226)
writing to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Mon Feb 15 16:52:36 EST 2021
Found 1 runs
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

 cp /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/orig/001.mgz /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/rawavg.mgz 

/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped

 mri_convert /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/rawavg.mgz /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/orig.mgz --conform 

mri_convert.bin /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/rawavg.mgz /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/orig.mgz --conform 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/rawavg.mgz...
TR=2530.00, TE=1.69, TI=1250.00, flip angle=7.00
i_ras = (0.039788, -0.992172, -0.118368)
j_ras = (-0.0644291, 0.115668, -0.991196)
k_ras = (-0.997129, -0.047064, 0.0593226)
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/orig.mgz...

 mri_add_xform_to_header -c /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/transforms/talairach.xfm /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/orig.mgz /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Mon Feb 15 16:52:45 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri

 mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 

/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri
/airflow/apps/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux mercury-224.braincode.ca 4.4.0-173-generic #203-Ubuntu SMP Wed Jan 15 02:55:01 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
Mon Feb 15 16:52:45 EST 2021
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.31971
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.31971/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.31971/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=2530.00, TE=1.69, TI=1250.00, flip angle=7.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (3.72529e-09, 8.84756e-09, -1)
k_ras = (0, 1, -1.04774e-08)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.31971/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Mon Feb 15 16:52:55 EST 2021
nu_correct -clobber ./tmp.mri_nu_correct.mni.31971/nu0.mnc ./tmp.mri_nu_correct.mni.31971/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.31971/0/ -iterations 1000 -distance 50
[airflow@mercury-224.braincode.ca:/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/] [2021-02-15 16:52:55] running:
  /airflow/apps/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.31971/0/ ./tmp.mri_nu_correct.mni.31971/nu0.mnc ./tmp.mri_nu_correct.mni.31971/nu1.imp

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Number of iterations: 49 
CV of field change: 0.00099335
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.31971/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.31971/nu1.mnc orig_nu.mgz --like orig.mgz --conform 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.31971/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (3.72529e-09, 8.84757e-09, -1)
k_ras = (0, 1, -1.04774e-08)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Mon Feb 15 16:54:19 EST 2021
mri_nu_correct.mni done

 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 

talairach_avi log file is transforms/talairach_avi.log...
Started at Mon Feb 15 16:54:19 EST 2021
Ended   at Mon Feb 15 16:54:45 EST 2021
talairach_avi done

 cp transforms/talairach.auto.xfm transforms/talairach.xfm 

#--------------------------------------------
#@# Talairach Failure Detection Mon Feb 15 16:54:47 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7186, pval=0.4932 >= threshold=0.0050)

 awk -f /airflow/apps/freesurfer/bin/extract_talairach_avi_QA.awk /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/transforms/talairach_avi.log 


 tal_QC_AZS /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/transforms/talairach_avi.log 

TalAviQA: 0.98104
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Mon Feb 15 16:54:47 EST 2021

 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 

/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri
/airflow/apps/freesurfer/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux mercury-224.braincode.ca 4.4.0-173-generic #203-Ubuntu SMP Wed Jan 15 02:55:01 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
Mon Feb 15 16:54:47 EST 2021
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.1166
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1166/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1166/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=2530.00, TE=1.69, TI=1250.00, flip angle=7.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (3.72529e-09, 8.84756e-09, -1)
k_ras = (0, 1, -1.04774e-08)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.1166/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Mon Feb 15 16:54:50 EST 2021
nu_correct -clobber ./tmp.mri_nu_correct.mni.1166/nu0.mnc ./tmp.mri_nu_correct.mni.1166/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1166/0/
[airflow@mercury-224.braincode.ca:/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/] [2021-02-15 16:54:50] running:
  /airflow/apps/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1166/0/ ./tmp.mri_nu_correct.mni.1166/nu0.mnc ./tmp.mri_nu_correct.mni.1166/nu1.imp

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Number of iterations: 48 
CV of field change: 0.000976575
 
 
--------------------------------------------------------
Iteration 2 Mon Feb 15 16:55:50 EST 2021
nu_correct -clobber ./tmp.mri_nu_correct.mni.1166/nu1.mnc ./tmp.mri_nu_correct.mni.1166/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.1166/1/
[airflow@mercury-224.braincode.ca:/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/] [2021-02-15 16:55:50] running:
  /airflow/apps/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1166/1/ ./tmp.mri_nu_correct.mni.1166/nu1.mnc ./tmp.mri_nu_correct.mni.1166/nu2.imp

Processing:.................................................................Done
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Processing:.................................................................Done
Number of iterations: 31 
CV of field change: 0.000976309
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.1166/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1166/ones.mgz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.1166/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1166/ones.mgz 
sysname  Linux
hostname mercury-224.braincode.ca
machine  x86_64
user     airflow

input      ./tmp.mri_nu_correct.mni.1166/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.1166/ones.mgz
Binarizing based on threshold
min        -1
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 16777216 values in range
Counting number of voxels in first frame
Found 16777216 voxels in final mask
Count: 16777216 16777216.000000 16777216 100.000000
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1166/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1166/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1166/input.mean.dat

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1166/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1166/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1166/input.mean.dat 
sysname  Linux
hostname mercury-224.braincode.ca
machine  x86_64
user     airflow
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.1166/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation

Reporting on   1 segmentations
Using PrintSegStat
Computing spatial average of each frame
  0
Writing to ./tmp.mri_nu_correct.mni.1166/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1166/ones.mgz --i ./tmp.mri_nu_correct.mni.1166/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1166/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1166/output.mean.dat

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1166/ones.mgz --i ./tmp.mri_nu_correct.mni.1166/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1166/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1166/output.mean.dat 
sysname  Linux
hostname mercury-224.braincode.ca
machine  x86_64
user     airflow
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.1166/ones.mgz
Loading ./tmp.mri_nu_correct.mni.1166/nu2.mnc
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation

Reporting on   1 segmentations
Using PrintSegStat
Computing spatial average of each frame
  0
Writing to ./tmp.mri_nu_correct.mni.1166/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.1166/nu2.mnc ./tmp.mri_nu_correct.mni.1166/nu2.mnc mul .86773087321251806886
Saving result to './tmp.mri_nu_correct.mni.1166/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.1166/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.1166/nu2.mnc nu.mgz --like orig.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.1166/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, -7.45058e-09)
j_ras = (3.72529e-09, 8.84757e-09, -1)
k_ras = (0, 1, -1.04774e-08)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 6 seconds.
mapping (17, 169) to ( 3, 110)
 
 
Mon Feb 15 16:57:07 EST 2021
mri_nu_correct.mni done

 mri_add_xform_to_header -c /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Mon Feb 15 16:57:08 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri

 mri_normalize -g 1 -mprage nu.mgz T1.mgz 

using max gradient = 1.000
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading from nu.mgz...
normalizing image...
talairach transform
 1.10287   0.05874  -0.06790  -4.09884;
-0.02651   0.98571   0.13654  -33.77138;
 0.07631  -0.16623   1.03266  -21.11436;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 22
Starting OpenSpline(): npoints = 22
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 90
gm peak at 68 (68), valley at 44 (44)
csf peak at 35, setting threshold to 57
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 82 (82), valley at 43 (43)
csf peak at 41, setting threshold to 68
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 1 minutes and 47 seconds.
#--------------------------------------------
#@# Skull Stripping Mon Feb 15 16:58:56 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri

 mri_em_register -rusage /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /airflow/apps/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta 

aligning to atlas containing skull, setting unknown_nbr_spacing = 5

== Number of threads available to mri_em_register for OpenMP = 1 == 
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/airflow/apps/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'...
average std = 22.9   using min determinant for regularization = 52.6
0 singular and 9002 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 8.7 or > 569.1 
total sample mean = 77.6 (1399 zeros)
************************************************
spacing=8, using 3243 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3243, passno 0, spacing 8
resetting wm mean[0]: 100 --> 108
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=13.0
skull bounding box = (47, 16, 22) --> (204, 255, 224)
using (99, 96, 123) as brain centroid...
mean wm in atlas = 108, using box (80,66,98) --> (118, 125,147) to find MRI wm
before smoothing, mri peak at 106
robust fit to distribution - 105 +- 6.2
after smoothing, mri peak at 105, scaling input intensities by 1.029
scaling channel 0 by 1.02857
initial log_p = -4.574
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.436434 @ (9.091, 27.273, -9.091)
max log p =    -4.407537 @ (-4.545, -4.545, 4.545)
max log p =    -4.359044 @ (-2.273, -2.273, -2.273)
max log p =    -4.352278 @ (1.136, 7.955, -1.136)
max log p =    -4.340630 @ (-1.705, -2.841, -0.568)
max log p =    -4.340630 @ (0.000, 0.000, 0.000)
Found translation: (1.7, 25.6, -8.5): log p = -4.341
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.144, old_max_log_p =-4.341 (thresh=-4.3)
 1.14016  -0.14816  -0.02206  -3.14786;
 0.15011   1.12538   0.16757  -27.55649;
 0.00000  -0.11161   0.99651   4.90877;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.133, old_max_log_p =-4.144 (thresh=-4.1)
 1.14033   0.01570  -0.12877  -1.90175;
 0.00127   1.13303   0.18597  -11.34318;
 0.14882  -0.13000   0.98511  -10.89464;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.133, old_max_log_p =-4.133 (thresh=-4.1)
 1.14033   0.01570  -0.12877  -1.90175;
 0.00127   1.13303   0.18597  -11.34318;
 0.14882  -0.13000   0.98511  -10.89464;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.085, old_max_log_p =-4.133 (thresh=-4.1)
 1.14508  -0.06695  -0.07609  -3.01915;
 0.07396   1.13458   0.15006  -14.28075;
 0.07499  -0.09043   0.97766  -7.35369;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.081, old_max_log_p =-4.085 (thresh=-4.1)
 1.16655  -0.06821  -0.07752  -5.41717;
 0.07723   1.10512   0.20968  -20.48416;
 0.07130  -0.16753   0.98386   2.98612;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.069, old_max_log_p =-4.081 (thresh=-4.1)
 1.16411  -0.05146  -0.06555  -8.48241;
 0.05925   1.10194   0.22655  -19.40261;
 0.06027  -0.18442   0.97744   7.10366;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.069, old_max_log_p =-4.069 (thresh=-4.1)
 1.16411  -0.05146  -0.06555  -8.48241;
 0.05925   1.10194   0.22655  -19.40261;
 0.06027  -0.18442   0.97744   7.10366;
 0.00000   0.00000   0.00000   1.00000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 3243 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.16411  -0.05146  -0.06555  -8.48241;
 0.05925   1.10194   0.22655  -19.40261;
 0.06027  -0.18442   0.97744   7.10366;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.16411  -0.05146  -0.06555  -8.48241;
 0.05925   1.10194   0.22655  -19.40261;
 0.06027  -0.18442   0.97744   7.10366;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.16411  -0.05146  -0.06555  -8.48241;
 0.05925   1.10194   0.22655  -19.40261;
 0.06027  -0.18442   0.97744   7.10366;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -4.069 (old=-4.574)
transform before final EM align:
 1.16411  -0.05146  -0.06555  -8.48241;
 0.05925   1.10194   0.22655  -19.40261;
 0.06027  -0.18442   0.97744   7.10366;
 0.00000   0.00000   0.00000   1.00000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 364799 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.16411  -0.05146  -0.06555  -8.48241;
 0.05925   1.10194   0.22655  -19.40261;
 0.06027  -0.18442   0.97744   7.10366;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.16411  -0.05146  -0.06555  -8.48241;
 0.05925   1.10194   0.22655  -19.40261;
 0.06027  -0.18442   0.97744   7.10366;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    4.4  tol 0.000000
final transform:
 1.16411  -0.05146  -0.06555  -8.48241;
 0.05925   1.10194   0.22655  -19.40261;
 0.06027  -0.18442   0.97744   7.10366;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    819.712000
mri_em_register stimesec    1.984000
mri_em_register ru_maxrss   612444
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   157470
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  0
mri_em_register ru_oublock  24
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    25
mri_em_register ru_nivcsw   9895
registration took 13 minutes and 42 seconds.

 mri_watershed -rusage /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/touch/rusage.mri_watershed.dat -T1 -brain_atlas /airflow/apps/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


Mode:          T1 normalized volume
Mode:          Use the information of atlas (default parms, --help for details)

*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed

*************************WATERSHED**************************
Sorting...
      first estimation of the COG coord: x=126 y=93 z=117 r=96
      first estimation of the main basin volume: 3771221 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        17 found in the rest of the brain 
      global maximum in x=148, y=90, z=73, Imax=255
      CSF=14, WM_intensity=110, WM_VARIANCE=5
      WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
      preflooding height equal to 10 percent
done.
Analyze...

      main basin size=456009505 voxels, voxel volume =1.000 
                     = 456009505 mmm3 = 456009.504 cm3
done.
PostAnalyze...Basin Prior
 9 basins merged thanks to atlas 
      ***** 0 basin(s) merged in 1 iteration(s)
      ***** 0 voxel(s) added to the main basin
done.
Weighting the input with prior template 

****************TEMPLATE DEFORMATION****************

      second estimation of the COG coord: x=125,y=97, z=112, r=10159 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=44 , nb = 43424
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1039246722
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1088902848
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=41 , nb = 1084770870
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=44 , nb = 1075939648
    OTHER      CSF_MIN=0, CSF_intensity=3, CSF_MAX=8 , nb = 1072814006
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    44,      49,        52,   73
  after  analyzing :    44,      51,        52,   56
   RIGHT_CER   
  before analyzing :    4,      4,        21,   87
  after  analyzing :    4,      18,        25,   35
   LEFT_CER    
  before analyzing :    5,      8,        50,   86
  after  analyzing :    5,      36,        50,   48
  RIGHT_BRAIN  
  before analyzing :    41,      47,        51,   72
  after  analyzing :    41,      49,        51,   54
  LEFT_BRAIN   
  before analyzing :    44,      50,        54,   73
  after  analyzing :    44,      52,        54,   57
     OTHER     
  before analyzing :    8,      14,        22,   28
  after  analyzing :    8,      21,        25,   22
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...62 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.010
curvature mean = 70.495, std = 7.577

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 2.47, sigma = 4.15
      after  rotation: sse = 2.47, sigma = 4.15
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  2.57, its var is  3.67   
      before Erosion-Dilatation  0.32% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...45 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1740566 voxels, voxel volume = 1.000 mm3
           = 1740566 mmm3 = 1740.566 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    16.916000
mri_watershed stimesec    0.384000
mri_watershed ru_maxrss   844192
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   214791
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  2720
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    51
mri_watershed ru_nivcsw   78
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Mon Feb 15 17:12:56 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri

 mri_em_register -rusage /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /airflow/apps/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta 

setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to mri_em_register for OpenMP = 1 == 
reading 1 input volumes...
logging results to talairach.log
reading '/airflow/apps/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
average std = 7.3   using min determinant for regularization = 5.3
0 singular and 841 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 6.3 or > 503.7 
total sample mean = 78.8 (1011 zeros)
************************************************
spacing=8, using 2830 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2830, passno 0, spacing 8
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=25.0
skull bounding box = (61, 32, 33) --> (188, 159, 209)
using (103, 74, 121) as brain centroid...
mean wm in atlas = 107, using box (87,58,99) --> (118, 89,142) to find MRI wm
before smoothing, mri peak at 104
robust fit to distribution - 104 +- 3.9
after smoothing, mri peak at 104, scaling input intensities by 1.029
scaling channel 0 by 1.02885
initial log_p = -4.366
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.069549 @ (9.091, 27.273, -9.091)
max log p =    -3.926715 @ (-4.545, -4.545, 4.545)
max log p =    -3.828436 @ (-2.273, 2.273, -6.818)
max log p =    -3.826043 @ (-1.136, 3.409, 5.682)
max log p =    -3.815774 @ (-0.568, -1.705, -1.705)
max log p =    -3.815774 @ (0.000, 0.000, 0.000)
Found translation: (0.6, 26.7, -7.4): log p = -3.816
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.751, old_max_log_p =-3.816 (thresh=-3.8)
 1.07500   0.00000   0.00000  -8.89450;
 0.00000   0.96593   0.25882  -6.84342;
 0.00000  -0.23941   0.89348   26.79787;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.749, old_max_log_p =-3.751 (thresh=-3.7)
 1.06580  -0.12092  -0.04872   9.92862;
 0.12979   0.84960   0.34228  -21.18564;
 0.00000  -0.39070   0.91596   39.32117;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.612, old_max_log_p =-3.749 (thresh=-3.7)
 1.08833  -0.09192  -0.04681   3.97206;
 0.09909   0.94784   0.23403  -12.82004;
 0.01130  -0.27057   0.93482   25.61316;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.612, old_max_log_p =-3.612 (thresh=-3.6)
 1.08833  -0.09192  -0.04681   3.97206;
 0.09909   0.94784   0.23403  -12.82004;
 0.01130  -0.27057   0.93482   25.61316;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.598, old_max_log_p =-3.612 (thresh=-3.6)
 1.09088  -0.09213  -0.04692   3.68433;
 0.09898   0.94672   0.23376  -12.66485;
 0.01134  -0.27152   0.93811   25.33228;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.598, old_max_log_p =-3.598 (thresh=-3.6)
 1.09088  -0.09213  -0.04692   3.68433;
 0.09898   0.94672   0.23376  -12.66485;
 0.01134  -0.27152   0.93811   25.33228;
 0.00000   0.00000   0.00000   1.00000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 2830 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.09088  -0.09213  -0.04692   3.68433;
 0.09898   0.94672   0.23376  -12.66485;
 0.01134  -0.27152   0.93811   25.33228;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.09088  -0.09213  -0.04692   3.68433;
 0.09898   0.94672   0.23376  -12.66485;
 0.01134  -0.27152   0.93811   25.33228;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.09088  -0.09213  -0.04692   3.68433;
 0.09898   0.94672   0.23376  -12.66485;
 0.01134  -0.27152   0.93811   25.33228;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.598 (old=-4.366)
transform before final EM align:
 1.09088  -0.09213  -0.04692   3.68433;
 0.09898   0.94672   0.23376  -12.66485;
 0.01134  -0.27152   0.93811   25.33228;
 0.00000   0.00000   0.00000   1.00000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 315557 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.09088  -0.09213  -0.04692   3.68433;
 0.09898   0.94672   0.23376  -12.66485;
 0.01134  -0.27152   0.93811   25.33228;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.09088  -0.09213  -0.04692   3.68433;
 0.09898   0.94672   0.23376  -12.66485;
 0.01134  -0.27152   0.93811   25.33228;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =    4.0  tol 0.000000
final transform:
 1.09088  -0.09213  -0.04692   3.68433;
 0.09898   0.94672   0.23376  -12.66485;
 0.01134  -0.27152   0.93811   25.33228;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    600.956000
mri_em_register stimesec    1.760000
mri_em_register ru_maxrss   601800
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   158210
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  0
mri_em_register ru_oublock  24
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    35
mri_em_register ru_nivcsw   8724
registration took 10 minutes and 3 seconds.
#--------------------------------------
#@# CA Normalize Mon Feb 15 17:22:59 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri

 mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /airflow/apps/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz 

writing control point volume to ctrl_pts.mgz
using MR volume brainmask.mgz to mask input volume...
reading 1 input volume
reading atlas from '/airflow/apps/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
reading transform from 'transforms/talairach.lta'...
reading input volume from nu.mgz...
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=25.0
skull bounding box = (61, 32, 33) --> (188, 159, 209)
using (103, 74, 121) as brain centroid...
mean wm in atlas = 107, using box (87,58,99) --> (118, 89,142) to find MRI wm
before smoothing, mri peak at 104
robust fit to distribution - 104 +- 3.9
after smoothing, mri peak at 104, scaling input intensities by 1.029
scaling channel 0 by 1.02885
using 246344 sample points...
INFO: compute sample coordinates transform
 1.09088  -0.09213  -0.04692   3.68433;
 0.09898   0.94672   0.23376  -12.66485;
 0.01134  -0.27152   0.93811   25.33228;
 0.00000   0.00000   0.00000   1.00000;
INFO: transform used
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (123, 30, 35) --> (187, 148, 204)
Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
0 of 5333 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (65, 32, 34) --> (128, 149, 205)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
1 of 5965 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (128, 124, 66) --> (175, 165, 122)
Left_Cerebellum_White_Matter: limiting intensities to 104.0 --> 132.0
0 of 62 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (89, 125, 64) --> (129, 168, 123)
Right_Cerebellum_White_Matter: limiting intensities to 111.0 --> 132.0
3 of 9 (33.3%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 109, 102) --> (146, 181, 134)
Brain_Stem: limiting intensities to 96.0 --> 132.0
0 of 156 (0.0%) samples deleted
using 11525 total control points for intensity normalization...
bias field = 0.953 +- 0.050
149 of 11521 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (123, 30, 35) --> (187, 148, 204)
Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 130.0
0 of 6672 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (65, 32, 34) --> (128, 149, 205)
Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 130.0
1 of 7073 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (128, 124, 66) --> (175, 165, 122)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 130.0
15 of 111 (13.5%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (89, 125, 64) --> (129, 168, 123)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 130.0
21 of 46 (45.7%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 109, 102) --> (146, 181, 134)
Brain_Stem: limiting intensities to 88.0 --> 130.0
0 of 211 (0.0%) samples deleted
using 14113 total control points for intensity normalization...
bias field = 1.041 +- 0.045
135 of 13983 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (123, 30, 35) --> (187, 148, 204)
Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 129.0
7 of 6878 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (65, 32, 34) --> (128, 149, 205)
Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 129.0
2 of 6992 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (128, 124, 66) --> (175, 165, 122)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 129.0
20 of 133 (15.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (89, 125, 64) --> (129, 168, 123)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 129.0
10 of 29 (34.5%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 109, 102) --> (146, 181, 134)
Brain_Stem: limiting intensities to 88.0 --> 129.0
10 of 227 (4.4%) samples deleted
using 14259 total control points for intensity normalization...
bias field = 1.033 +- 0.039
114 of 14014 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 19 seconds.
#--------------------------------------
#@# CA Reg Mon Feb 15 17:24:19 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri

 mri_ca_register -rusage /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /airflow/apps/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z 

not handling expanded ventricles...
using previously computed transform transforms/talairach.lta
renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-regularize_mean 0.500
	-regularize 0.500
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to mri_ca_register for OpenMP = 1 == 
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/airflow/apps/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.05 (predicted orig area = 7.6)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.899, neg=0, invalid=762
0001: dt=263.075113, rms=0.813 (9.549%), neg=0, invalid=762
0002: dt=238.623656, rms=0.776 (4.576%), neg=0, invalid=762
0003: dt=137.677419, rms=0.758 (2.301%), neg=0, invalid=762
0004: dt=295.936000, rms=0.746 (1.556%), neg=0, invalid=762
0005: dt=129.472000, rms=0.739 (1.011%), neg=0, invalid=762
0006: dt=295.936000, rms=0.733 (0.766%), neg=0, invalid=762
0007: dt=129.472000, rms=0.729 (0.565%), neg=0, invalid=762
0008: dt=295.936000, rms=0.725 (0.501%), neg=0, invalid=762
0009: dt=129.472000, rms=0.722 (0.394%), neg=0, invalid=762
0010: dt=295.936000, rms=0.720 (0.321%), neg=0, invalid=762
0011: dt=129.472000, rms=0.718 (0.272%), neg=0, invalid=762
0012: dt=221.952000, rms=0.717 (0.202%), neg=0, invalid=762
0013: dt=221.952000, rms=0.716 (0.154%), neg=0, invalid=762
0014: dt=221.952000, rms=0.713 (0.426%), neg=0, invalid=762
0015: dt=221.952000, rms=0.710 (0.301%), neg=0, invalid=762
0016: dt=221.952000, rms=0.707 (0.462%), neg=0, invalid=762
0017: dt=221.952000, rms=0.705 (0.354%), neg=0, invalid=762
0018: dt=221.952000, rms=0.703 (0.301%), neg=0, invalid=762
0019: dt=221.952000, rms=0.701 (0.287%), neg=0, invalid=762
0020: dt=221.952000, rms=0.699 (0.173%), neg=0, invalid=762
0021: dt=221.952000, rms=0.698 (0.223%), neg=0, invalid=762
0022: dt=221.952000, rms=0.697 (0.165%), neg=0, invalid=762
0023: dt=221.952000, rms=0.695 (0.162%), neg=0, invalid=762
0024: dt=221.952000, rms=0.694 (0.141%), neg=0, invalid=762
0025: dt=221.952000, rms=0.694 (0.032%), neg=0, invalid=762
0026: dt=221.952000, rms=0.694 (0.108%), neg=0, invalid=762
0027: dt=221.952000, rms=0.693 (0.101%), neg=0, invalid=762
0028: dt=129.472000, rms=0.692 (0.046%), neg=0, invalid=762
0029: dt=129.472000, rms=0.692 (0.028%), neg=0, invalid=762
0030: dt=129.472000, rms=0.692 (0.078%), neg=0, invalid=762
0031: dt=129.472000, rms=0.691 (0.097%), neg=0, invalid=762
0032: dt=129.472000, rms=0.690 (0.099%), neg=0, invalid=762
0033: dt=129.472000, rms=0.690 (0.103%), neg=0, invalid=762
0034: dt=129.472000, rms=0.689 (0.084%), neg=0, invalid=762
0035: dt=129.472000, rms=0.689 (0.078%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.689, neg=0, invalid=762
0036: dt=221.952000, rms=0.686 (0.517%), neg=0, invalid=762
0037: dt=129.472000, rms=0.685 (0.084%), neg=0, invalid=762
0038: dt=129.472000, rms=0.685 (0.046%), neg=0, invalid=762
0039: dt=129.472000, rms=0.684 (0.083%), neg=0, invalid=762
0040: dt=129.472000, rms=0.683 (0.098%), neg=0, invalid=762
0041: dt=129.472000, rms=0.683 (0.092%), neg=0, invalid=762
0042: dt=129.472000, rms=0.682 (0.105%), neg=0, invalid=762
0043: dt=129.472000, rms=0.681 (0.095%), neg=0, invalid=762
0044: dt=1183.744000, rms=0.681 (0.073%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.692, neg=0, invalid=762
0045: dt=36.288000, rms=0.690 (0.344%), neg=0, invalid=762
0046: dt=193.306122, rms=0.685 (0.706%), neg=0, invalid=762
0047: dt=219.695906, rms=0.670 (2.130%), neg=0, invalid=762
0048: dt=33.630573, rms=0.667 (0.419%), neg=0, invalid=762
0049: dt=24.000000, rms=0.667 (0.048%), neg=0, invalid=762
0050: dt=24.000000, rms=0.667 (0.012%), neg=0, invalid=762
0051: dt=24.000000, rms=0.667 (0.048%), neg=0, invalid=762
0052: dt=24.000000, rms=0.666 (0.061%), neg=0, invalid=762
0053: dt=24.000000, rms=0.665 (0.179%), neg=0, invalid=762
0054: dt=24.000000, rms=0.663 (0.339%), neg=0, invalid=762
0055: dt=24.000000, rms=0.660 (0.497%), neg=0, invalid=762
0056: dt=24.000000, rms=0.656 (0.502%), neg=0, invalid=762
0057: dt=24.000000, rms=0.653 (0.443%), neg=0, invalid=762
0058: dt=24.000000, rms=0.651 (0.354%), neg=0, invalid=762
0059: dt=24.000000, rms=0.649 (0.271%), neg=0, invalid=762
0060: dt=24.000000, rms=0.648 (0.210%), neg=0, invalid=762
0061: dt=24.000000, rms=0.647 (0.195%), neg=0, invalid=762
0062: dt=24.000000, rms=0.645 (0.217%), neg=0, invalid=762
0063: dt=24.000000, rms=0.644 (0.252%), neg=0, invalid=762
0064: dt=24.000000, rms=0.642 (0.256%), neg=0, invalid=762
0065: dt=24.000000, rms=0.641 (0.226%), neg=0, invalid=762
0066: dt=24.000000, rms=0.639 (0.197%), neg=0, invalid=762
0067: dt=24.000000, rms=0.638 (0.158%), neg=0, invalid=762
0068: dt=24.000000, rms=0.637 (0.134%), neg=0, invalid=762
0069: dt=24.000000, rms=0.637 (0.119%), neg=0, invalid=762
0070: dt=24.000000, rms=0.636 (0.151%), neg=0, invalid=762
0071: dt=24.000000, rms=0.635 (0.133%), neg=0, invalid=762
0072: dt=24.000000, rms=0.634 (0.114%), neg=0, invalid=762
0073: dt=24.000000, rms=0.633 (0.103%), neg=0, invalid=762
0074: dt=82.944000, rms=0.633 (0.037%), neg=0, invalid=762
0075: dt=82.944000, rms=0.633 (0.068%), neg=0, invalid=762
0076: dt=82.944000, rms=0.633 (0.037%), neg=0, invalid=762
0077: dt=82.944000, rms=0.632 (0.017%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.633, neg=0, invalid=762
0078: dt=99.945205, rms=0.629 (0.578%), neg=0, invalid=762
0079: dt=25.920000, rms=0.629 (0.073%), neg=0, invalid=762
0080: dt=25.920000, rms=0.629 (0.012%), neg=0, invalid=762
0081: dt=25.920000, rms=0.629 (0.013%), neg=0, invalid=762
0082: dt=25.920000, rms=0.629 (0.019%), neg=0, invalid=762
0083: dt=25.920000, rms=0.628 (0.052%), neg=0, invalid=762
0084: dt=25.920000, rms=0.628 (0.075%), neg=0, invalid=762
0085: dt=25.920000, rms=0.627 (0.051%), neg=0, invalid=762
0086: dt=25.920000, rms=0.627 (0.051%), neg=0, invalid=762
0087: dt=25.920000, rms=0.627 (0.028%), neg=0, invalid=762
0088: dt=62.208000, rms=0.627 (0.036%), neg=0, invalid=762
0089: dt=414.720000, rms=0.626 (0.100%), neg=0, invalid=762
0090: dt=36.288000, rms=0.626 (0.050%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.658, neg=0, invalid=762
0091: dt=2.800000, rms=0.658 (0.087%), neg=0, invalid=762
0092: dt=1.200000, rms=0.658 (0.000%), neg=0, invalid=762
0093: dt=1.200000, rms=0.657 (0.018%), neg=0, invalid=762
0094: dt=1.200000, rms=0.657 (-0.010%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.658, neg=0, invalid=762
0095: dt=1.600000, rms=0.657 (0.087%), neg=0, invalid=762
0096: dt=0.600000, rms=0.657 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.746, neg=0, invalid=762
0097: dt=6.463768, rms=0.724 (3.033%), neg=0, invalid=762
0098: dt=7.587922, rms=0.720 (0.561%), neg=0, invalid=762
0099: dt=4.800000, rms=0.719 (0.056%), neg=0, invalid=762
0100: dt=4.800000, rms=0.719 (0.065%), neg=0, invalid=762
0101: dt=4.800000, rms=0.718 (0.021%), neg=0, invalid=762
0102: dt=4.800000, rms=0.719 (-0.139%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.719, neg=0, invalid=762
0103: dt=0.000000, rms=0.719 (0.050%), neg=0, invalid=762
0104: dt=0.000000, rms=0.719 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 5.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.781, neg=0, invalid=762
0105: dt=0.000000, rms=0.781 (0.043%), neg=0, invalid=762
0106: dt=0.000000, rms=0.781 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.781, neg=0, invalid=762
0107: dt=0.000000, rms=0.781 (0.043%), neg=0, invalid=762
0108: dt=0.000000, rms=0.781 (0.000%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 10.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.674, neg=0, invalid=762
0109: dt=0.801353, rms=0.658 (2.409%), neg=0, invalid=762
0110: dt=0.080000, rms=0.657 (0.125%), neg=0, invalid=762
0111: dt=0.080000, rms=0.657 (-0.101%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.657, neg=0, invalid=762
0112: dt=0.028000, rms=0.657 (0.071%), neg=0, invalid=762
0113: dt=0.000000, rms=0.657 (0.001%), neg=0, invalid=762
0114: dt=0.050000, rms=0.657 (-0.033%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.20629 (21)
Left_Lateral_Ventricle (4): linear fit = 1.16 x + 0.0 (1213 voxels, overlap=0.541)
Left_Lateral_Ventricle (4): linear fit = 1.16 x + 0.0 (1213 voxels, peak = 23), gca=23.3
gca peak = 0.15565 (16)
mri peak = 0.19411 (20)
Right_Lateral_Ventricle (43): linear fit = 1.27 x + 0.0 (1119 voxels, overlap=0.446)
Right_Lateral_Ventricle (43): linear fit = 1.27 x + 0.0 (1119 voxels, peak = 20), gca=20.4
gca peak = 0.26829 (96)
mri peak = 0.08216 (99)
Right_Pallidum (52): linear fit = 1.04 x + 0.0 (982 voxels, overlap=0.358)
Right_Pallidum (52): linear fit = 1.04 x + 0.0 (982 voxels, peak = 100), gca=100.3
gca peak = 0.20183 (93)
mri peak = 0.07777 (103)
Left_Pallidum (13): linear fit = 1.09 x + 0.0 (909 voxels, overlap=1.016)
Left_Pallidum (13): linear fit = 1.09 x + 0.0 (909 voxels, peak = 101), gca=100.9
gca peak = 0.21683 (55)
mri peak = 0.07262 (74)
Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (990 voxels, overlap=0.014)
Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (990 voxels, peak = 70), gca=70.1
gca peak = 0.30730 (58)
mri peak = 0.10784 (73)
Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (1019 voxels, overlap=0.012)
Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (1019 voxels, peak = 73), gca=72.8
gca peak = 0.11430 (101)
mri peak = 0.13125 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (77399 voxels, overlap=0.619)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (77399 voxels, peak = 104), gca=103.5
gca peak = 0.12076 (102)
mri peak = 0.11798 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (80096 voxels, overlap=0.656)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (80096 voxels, peak = 105), gca=104.5
gca peak = 0.14995 (59)
mri peak = 0.04097 (77)
Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (29540 voxels, overlap=0.001)
Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (29540 voxels, peak = 76), gca=76.4
gca peak = 0.15082 (58)
mri peak = 0.04369 (72)
Right_Cerebral_Cortex (42): linear fit = 1.27 x + 0.0 (29928 voxels, overlap=0.001)
Right_Cerebral_Cortex (42): linear fit = 1.27 x + 0.0 (29928 voxels, peak = 74), gca=73.9
gca peak = 0.14161 (67)
mri peak = 0.09581 (82)
Right_Caudate (50): linear fit = 1.20 x + 0.0 (1138 voxels, overlap=0.034)
Right_Caudate (50): linear fit = 1.20 x + 0.0 (1138 voxels, peak = 80), gca=80.1
gca peak = 0.15243 (71)
mri peak = 0.09205 (88)
Left_Caudate (11): linear fit = 1.17 x + 0.0 (1185 voxels, overlap=0.149)
Left_Caudate (11): linear fit = 1.17 x + 0.0 (1185 voxels, peak = 83), gca=83.4
gca peak = 0.13336 (57)
mri peak = 0.04055 (77)
Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (17187 voxels, overlap=0.001)
Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (17187 voxels, peak = 78), gca=78.4
gca peak = 0.13252 (56)
mri peak = 0.05183 (93)
Right_Cerebellum_Cortex (47): linear fit = 1.62 x + 0.0 (21515 voxels, overlap=0.001)
Right_Cerebellum_Cortex (47): linear fit = 1.62 x + 0.0 (21515 voxels, peak = 90), gca=90.4
gca peak = 0.18181 (84)
mri peak = 0.05259 (92)
Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (8423 voxels, overlap=0.001)
Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (8423 voxels, peak = 92), gca=92.0
gca peak = 0.20573 (83)
mri peak = 0.03202 (74)
Right_Cerebellum_White_Matter (46): linear fit = 0.94 x + 0.0 (5743 voxels, overlap=0.354)
Right_Cerebellum_White_Matter (46): linear fit = 0.94 x + 0.0 (5743 voxels, peak = 78), gca=77.6
gca peak = 0.21969 (57)
mri peak = 0.08539 (75)
Left_Amygdala (18): linear fit = 1.33 x + 0.0 (570 voxels, overlap=0.061)
Left_Amygdala (18): linear fit = 1.33 x + 0.0 (570 voxels, peak = 76), gca=75.5
gca peak = 0.39313 (56)
mri peak = 0.09567 (67)
Right_Amygdala (54): linear fit = 1.21 x + 0.0 (585 voxels, overlap=0.107)
Right_Amygdala (54): linear fit = 1.21 x + 0.0 (585 voxels, peak = 67), gca=67.5
gca peak = 0.14181 (85)
mri peak = 0.06803 (98)
Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (6406 voxels, overlap=0.242)
Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (6406 voxels, peak = 96), gca=96.5
gca peak = 0.11978 (83)
mri peak = 0.07960 (95)
Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5342 voxels, overlap=0.250)
Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5342 voxels, peak = 93), gca=93.4
gca peak = 0.13399 (79)
mri peak = 0.07265 (95)
Left_Putamen (12): linear fit = 1.20 x + 0.0 (2783 voxels, overlap=0.010)
Left_Putamen (12): linear fit = 1.20 x + 0.0 (2783 voxels, peak = 94), gca=94.4
gca peak = 0.14159 (79)
mri peak = 0.06967 (87)
Right_Putamen (51): linear fit = 1.14 x + 0.0 (2813 voxels, overlap=0.376)
Right_Putamen (51): linear fit = 1.14 x + 0.0 (2813 voxels, peak = 90), gca=90.5
gca peak = 0.10025 (80)
mri peak = 0.09738 (93)
Brain_Stem (16): linear fit = 1.15 x + 0.0 (8976 voxels, overlap=0.029)
Brain_Stem (16): linear fit = 1.15 x + 0.0 (8976 voxels, peak = 92), gca=92.4
gca peak = 0.13281 (86)
mri peak = 0.11523 (99)
Right_VentralDC (60): linear fit = 1.14 x + 0.0 (1220 voxels, overlap=0.014)
Right_VentralDC (60): linear fit = 1.14 x + 0.0 (1220 voxels, peak = 98), gca=98.5
gca peak = 0.12801 (89)
mri peak = 0.09157 (97)
Left_VentralDC (28): linear fit = 1.13 x + 0.0 (1254 voxels, overlap=0.131)
Left_VentralDC (28): linear fit = 1.13 x + 0.0 (1254 voxels, peak = 101), gca=101.0
gca peak = 0.20494 (23)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.15061 (21)
mri peak = 0.12123 (29)
Fourth_Ventricle (15): linear fit = 1.53 x + 0.0 (660 voxels, overlap=0.546)
Fourth_Ventricle (15): linear fit = 1.53 x + 0.0 (660 voxels, peak = 32), gca=32.2
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18056 (32)
gca peak Left_Thalamus = 0.64095 (94)
gca peak Third_Ventricle = 0.20494 (23)
gca peak Fourth_Ventricle = 0.15061 (21)
gca peak CSF = 0.20999 (34)
gca peak Left_Accumbens_area = 0.39030 (62)
gca peak Left_undetermined = 0.95280 (25)
gca peak Left_vessel = 0.67734 (53)
gca peak Left_choroid_plexus = 0.09433 (44)
gca peak Right_Inf_Lat_Vent = 0.23544 (26)
gca peak Right_Cerebellum_Cortex = 0.13252 (56)
gca peak Right_Accumbens_area = 0.30312 (64)
gca peak Right_vessel = 0.46315 (51)
gca peak Right_choroid_plexus = 0.14086 (44)
gca peak Fifth_Ventricle = 0.51669 (36)
gca peak WM_hypointensities = 0.09722 (76)
gca peak non_WM_hypointensities = 0.11899 (47)
gca peak Optic_Chiasm = 0.39033 (72)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
setting label Right_Cerebellum_Cortex based on Left_Cerebellum_Cortex = 1.38 x +  0: 78
estimating mean gm scale to be 1.27 x + 0.0
estimating mean wm scale to be 1.02 x + 0.0
estimating mean csf scale to be 1.22 x + 0.0
Left_Putamen too bright - rescaling by 0.992 (from 1.195) to 93.6 (was 94.4)
Left_Pallidum too bright - rescaling by 1.000 (from 1.085) to 100.9 (was 100.9)
saving intensity scales to talairach.label_intensities.txt
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.658, neg=0, invalid=762
0115: dt=114.389414, rms=0.631 (4.155%), neg=0, invalid=762
0116: dt=246.390760, rms=0.623 (1.282%), neg=0, invalid=762
0117: dt=295.936000, rms=0.618 (0.758%), neg=0, invalid=762
0118: dt=129.472000, rms=0.615 (0.571%), neg=0, invalid=762
0119: dt=517.888000, rms=0.612 (0.436%), neg=0, invalid=762
0120: dt=129.472000, rms=0.610 (0.359%), neg=0, invalid=762
0121: dt=129.472000, rms=0.609 (0.079%), neg=0, invalid=762
0122: dt=369.920000, rms=0.608 (0.174%), neg=0, invalid=762
0123: dt=92.480000, rms=0.608 (0.111%), neg=0, invalid=762
0124: dt=443.904000, rms=0.607 (0.118%), neg=0, invalid=762
0125: dt=92.480000, rms=0.606 (0.119%), neg=0, invalid=762
0126: dt=443.904000, rms=0.605 (0.101%), neg=0, invalid=762
0127: dt=92.480000, rms=0.605 (0.085%), neg=0, invalid=762
0128: dt=443.904000, rms=0.604 (0.106%), neg=0, invalid=762
0129: dt=73.984000, rms=0.604 (0.058%), neg=0, invalid=762
0130: dt=1479.680000, rms=0.603 (0.177%), neg=0, invalid=762
0131: dt=92.480000, rms=0.602 (0.127%), neg=0, invalid=762
0132: dt=295.936000, rms=0.602 (0.066%), neg=0, invalid=762
0133: dt=110.976000, rms=0.602 (0.034%), neg=0, invalid=762
0134: dt=110.976000, rms=0.601 (0.008%), neg=0, invalid=762
0135: dt=110.976000, rms=0.601 (0.021%), neg=0, invalid=762
0136: dt=110.976000, rms=0.601 (0.050%), neg=0, invalid=762
0137: dt=110.976000, rms=0.601 (0.059%), neg=0, invalid=762
0138: dt=110.976000, rms=0.600 (0.067%), neg=0, invalid=762
0139: dt=110.976000, rms=0.600 (0.073%), neg=0, invalid=762
0140: dt=110.976000, rms=0.599 (0.076%), neg=0, invalid=762
0141: dt=110.976000, rms=0.599 (0.078%), neg=0, invalid=762
0142: dt=110.976000, rms=0.599 (0.069%), neg=0, invalid=762
0143: dt=110.976000, rms=0.598 (0.074%), neg=0, invalid=762
0144: dt=110.976000, rms=0.598 (0.069%), neg=0, invalid=762
0145: dt=110.976000, rms=0.597 (0.066%), neg=0, invalid=762
0146: dt=110.976000, rms=0.597 (0.064%), neg=0, invalid=762
0147: dt=110.976000, rms=0.596 (0.066%), neg=0, invalid=762
0148: dt=110.976000, rms=0.596 (0.068%), neg=0, invalid=762
0149: dt=110.976000, rms=0.596 (0.062%), neg=0, invalid=762
0150: dt=110.976000, rms=0.595 (0.061%), neg=0, invalid=762
0151: dt=110.976000, rms=0.595 (0.056%), neg=0, invalid=762
0152: dt=110.976000, rms=0.595 (0.051%), neg=0, invalid=762
0153: dt=110.976000, rms=0.594 (0.051%), neg=0, invalid=762
0154: dt=110.976000, rms=0.594 (0.048%), neg=0, invalid=762
0155: dt=110.976000, rms=0.594 (0.046%), neg=0, invalid=762
0156: dt=110.976000, rms=0.594 (0.048%), neg=0, invalid=762
0157: dt=110.976000, rms=0.593 (0.051%), neg=0, invalid=762
0158: dt=110.976000, rms=0.593 (0.044%), neg=0, invalid=762
0159: dt=110.976000, rms=0.593 (0.046%), neg=0, invalid=762
0160: dt=110.976000, rms=0.592 (0.043%), neg=0, invalid=762
0161: dt=110.976000, rms=0.592 (0.040%), neg=0, invalid=762
0162: dt=110.976000, rms=0.592 (0.044%), neg=0, invalid=762
0163: dt=110.976000, rms=0.592 (0.044%), neg=0, invalid=762
0164: dt=110.976000, rms=0.591 (0.038%), neg=0, invalid=762
0165: dt=110.976000, rms=0.591 (0.036%), neg=0, invalid=762
0166: dt=110.976000, rms=0.591 (0.034%), neg=0, invalid=762
0167: dt=110.976000, rms=0.591 (0.035%), neg=0, invalid=762
0168: dt=110.976000, rms=0.591 (0.036%), neg=0, invalid=762
0169: dt=110.976000, rms=0.590 (0.035%), neg=0, invalid=762
0170: dt=110.976000, rms=0.590 (0.036%), neg=0, invalid=762
0171: dt=110.976000, rms=0.590 (0.032%), neg=0, invalid=762
0172: dt=110.976000, rms=0.590 (0.030%), neg=0, invalid=762
0173: dt=110.976000, rms=0.590 (0.028%), neg=0, invalid=762
0174: dt=110.976000, rms=0.590 (0.023%), neg=0, invalid=762
0175: dt=110.976000, rms=0.589 (0.021%), neg=0, invalid=762
0176: dt=0.361250, rms=0.589 (0.001%), neg=0, invalid=762
0177: dt=0.361250, rms=0.589 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.590, neg=0, invalid=762
0178: dt=369.920000, rms=0.588 (0.196%), neg=0, invalid=762
0179: dt=129.472000, rms=0.588 (0.090%), neg=0, invalid=762
0180: dt=129.472000, rms=0.588 (0.010%), neg=0, invalid=762
0181: dt=129.472000, rms=0.588 (0.023%), neg=0, invalid=762
0182: dt=129.472000, rms=0.588 (0.028%), neg=0, invalid=762
0183: dt=129.472000, rms=0.587 (0.037%), neg=0, invalid=762
0184: dt=129.472000, rms=0.587 (0.041%), neg=0, invalid=762
0185: dt=129.472000, rms=0.587 (0.057%), neg=0, invalid=762
0186: dt=129.472000, rms=0.587 (0.046%), neg=0, invalid=762
0187: dt=129.472000, rms=0.586 (0.034%), neg=0, invalid=762
0188: dt=129.472000, rms=0.586 (0.030%), neg=0, invalid=762
0189: dt=129.472000, rms=0.586 (0.038%), neg=0, invalid=762
0190: dt=129.472000, rms=0.586 (0.047%), neg=0, invalid=762
0191: dt=129.472000, rms=0.585 (0.030%), neg=0, invalid=762
0192: dt=129.472000, rms=0.585 (0.027%), neg=0, invalid=762
0193: dt=129.472000, rms=0.585 (0.023%), neg=0, invalid=762
0194: dt=129.472000, rms=0.585 (0.037%), neg=0, invalid=762
0195: dt=129.472000, rms=0.585 (0.037%), neg=0, invalid=762
0196: dt=129.472000, rms=0.585 (0.029%), neg=0, invalid=762
0197: dt=129.472000, rms=0.584 (0.019%), neg=0, invalid=762
0198: dt=129.472000, rms=0.584 (0.012%), neg=0, invalid=762
0199: dt=295.936000, rms=0.584 (0.031%), neg=0, invalid=762
0200: dt=18.496000, rms=0.584 (0.002%), neg=0, invalid=762
0201: dt=18.496000, rms=0.584 (-0.003%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.585, neg=0, invalid=762
0202: dt=115.770701, rms=0.583 (0.377%), neg=0, invalid=762
0203: dt=145.152000, rms=0.579 (0.750%), neg=0, invalid=762
0204: dt=36.288000, rms=0.578 (0.187%), neg=0, invalid=762
0205: dt=414.720000, rms=0.573 (0.703%), neg=0, invalid=762
0206: dt=81.454545, rms=0.570 (0.609%), neg=0, invalid=762
0207: dt=36.288000, rms=0.569 (0.237%), neg=0, invalid=762
0208: dt=145.152000, rms=0.567 (0.257%), neg=0, invalid=762
0209: dt=89.503759, rms=0.566 (0.205%), neg=0, invalid=762
0210: dt=36.288000, rms=0.565 (0.092%), neg=0, invalid=762
0211: dt=580.608000, rms=0.562 (0.576%), neg=0, invalid=762
0212: dt=36.288000, rms=0.560 (0.311%), neg=0, invalid=762
0213: dt=103.680000, rms=0.560 (0.153%), neg=0, invalid=762
0214: dt=124.416000, rms=0.559 (0.106%), neg=0, invalid=762
0215: dt=82.944000, rms=0.558 (0.107%), neg=0, invalid=762
0216: dt=124.416000, rms=0.558 (0.107%), neg=0, invalid=762
0217: dt=82.944000, rms=0.557 (0.090%), neg=0, invalid=762
0218: dt=103.680000, rms=0.557 (0.085%), neg=0, invalid=762
0219: dt=62.208000, rms=0.556 (0.075%), neg=0, invalid=762
0220: dt=145.152000, rms=0.556 (0.115%), neg=0, invalid=762
0221: dt=36.288000, rms=0.556 (0.042%), neg=0, invalid=762
0222: dt=36.288000, rms=0.555 (0.028%), neg=0, invalid=762
0223: dt=36.288000, rms=0.555 (0.042%), neg=0, invalid=762
0224: dt=36.288000, rms=0.555 (0.069%), neg=0, invalid=762
0225: dt=36.288000, rms=0.554 (0.090%), neg=0, invalid=762
0226: dt=36.288000, rms=0.554 (0.106%), neg=0, invalid=762
0227: dt=36.288000, rms=0.553 (0.112%), neg=0, invalid=762
0228: dt=36.288000, rms=0.552 (0.119%), neg=0, invalid=762
0229: dt=36.288000, rms=0.552 (0.116%), neg=0, invalid=762
0230: dt=36.288000, rms=0.551 (0.124%), neg=0, invalid=762
0231: dt=36.288000, rms=0.550 (0.121%), neg=0, invalid=762
0232: dt=36.288000, rms=0.550 (0.120%), neg=0, invalid=762
0233: dt=36.288000, rms=0.549 (0.111%), neg=0, invalid=762
0234: dt=36.288000, rms=0.549 (0.113%), neg=0, invalid=762
0235: dt=36.288000, rms=0.548 (0.116%), neg=0, invalid=762
0236: dt=36.288000, rms=0.547 (0.106%), neg=0, invalid=762
0237: dt=36.288000, rms=0.547 (0.103%), neg=0, invalid=762
0238: dt=36.288000, rms=0.546 (0.103%), neg=0, invalid=762
0239: dt=36.288000, rms=0.546 (0.105%), neg=0, invalid=762
0240: dt=36.288000, rms=0.545 (0.098%), neg=0, invalid=762
0241: dt=36.288000, rms=0.545 (0.097%), neg=0, invalid=762
0242: dt=36.288000, rms=0.545 (0.007%), neg=0, invalid=762
0243: dt=36.288000, rms=0.544 (0.013%), neg=0, invalid=762
0244: dt=36.288000, rms=0.544 (0.022%), neg=0, invalid=762
0245: dt=36.288000, rms=0.544 (0.034%), neg=0, invalid=762
0246: dt=36.288000, rms=0.544 (0.034%), neg=0, invalid=762
0247: dt=36.288000, rms=0.544 (0.033%), neg=0, invalid=762
0248: dt=36.288000, rms=0.544 (0.031%), neg=0, invalid=762
0249: dt=36.288000, rms=0.543 (0.037%), neg=0, invalid=762
0250: dt=36.288000, rms=0.543 (0.040%), neg=0, invalid=762
0251: dt=36.288000, rms=0.543 (0.048%), neg=0, invalid=762
0252: dt=36.288000, rms=0.543 (0.053%), neg=0, invalid=762
0253: dt=36.288000, rms=0.542 (0.053%), neg=0, invalid=762
0254: dt=36.288000, rms=0.542 (0.053%), neg=0, invalid=762
0255: dt=36.288000, rms=0.542 (0.049%), neg=0, invalid=762
0256: dt=36.288000, rms=0.542 (0.048%), neg=0, invalid=762
0257: dt=36.288000, rms=0.541 (0.050%), neg=0, invalid=762
0258: dt=36.288000, rms=0.541 (0.051%), neg=0, invalid=762
0259: dt=36.288000, rms=0.541 (0.007%), neg=0, invalid=762
0260: dt=9.072000, rms=0.541 (0.002%), neg=0, invalid=762
0261: dt=2.268000, rms=0.541 (0.003%), neg=0, invalid=762
0262: dt=1.944000, rms=0.541 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.541, neg=0, invalid=762
0263: dt=0.141750, rms=0.541 (0.047%), neg=0, invalid=762
0264: dt=0.101250, rms=0.541 (0.001%), neg=0, invalid=762
0265: dt=0.000396, rms=0.541 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.548, neg=0, invalid=762
0266: dt=152.275862, rms=0.534 (2.492%), neg=0, invalid=762
0267: dt=38.400000, rms=0.529 (0.977%), neg=0, invalid=762
0268: dt=25.600000, rms=0.527 (0.372%), neg=0, invalid=762
0269: dt=44.800000, rms=0.525 (0.354%), neg=0, invalid=762
0270: dt=24.569288, rms=0.524 (0.287%), neg=0, invalid=762
0271: dt=38.400000, rms=0.523 (0.231%), neg=0, invalid=762
0272: dt=25.600000, rms=0.521 (0.228%), neg=0, invalid=762
0273: dt=32.000000, rms=0.520 (0.189%), neg=0, invalid=762
0274: dt=38.400000, rms=0.519 (0.198%), neg=0, invalid=762
0275: dt=24.872727, rms=0.518 (0.161%), neg=0, invalid=762
0276: dt=44.800000, rms=0.518 (0.183%), neg=0, invalid=762
0277: dt=23.148936, rms=0.517 (0.143%), neg=0, invalid=762
0278: dt=44.800000, rms=0.516 (0.175%), neg=0, invalid=762
0279: dt=25.600000, rms=0.515 (0.113%), neg=0, invalid=762
0280: dt=38.400000, rms=0.515 (0.125%), neg=0, invalid=762
0281: dt=25.600000, rms=0.514 (0.109%), neg=0, invalid=762
0282: dt=44.800000, rms=0.514 (0.113%), neg=0, invalid=762
0283: dt=11.200000, rms=0.513 (0.083%), neg=0, invalid=762
0284: dt=9.600000, rms=0.513 (0.028%), neg=0, invalid=762
0285: dt=0.600000, rms=0.513 (0.002%), neg=0, invalid=762
0286: dt=0.018750, rms=0.513 (0.002%), neg=0, invalid=762
0287: dt=0.009375, rms=0.513 (0.000%), neg=0, invalid=762
0288: dt=0.002344, rms=0.513 (0.000%), neg=0, invalid=762
0289: dt=0.000488, rms=0.513 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.513, neg=0, invalid=762
0290: dt=84.301075, rms=0.509 (0.794%), neg=0, invalid=762
0291: dt=30.431373, rms=0.508 (0.249%), neg=0, invalid=762
0292: dt=44.800000, rms=0.507 (0.147%), neg=0, invalid=762
0293: dt=32.000000, rms=0.506 (0.124%), neg=0, invalid=762
0294: dt=38.400000, rms=0.506 (0.115%), neg=0, invalid=762
0295: dt=25.600000, rms=0.505 (0.100%), neg=0, invalid=762
0296: dt=44.800000, rms=0.505 (0.084%), neg=0, invalid=762
0297: dt=32.000000, rms=0.504 (0.111%), neg=0, invalid=762
0298: dt=32.000000, rms=0.504 (0.077%), neg=0, invalid=762
0299: dt=38.400000, rms=0.504 (0.091%), neg=0, invalid=762
0300: dt=25.600000, rms=0.503 (0.059%), neg=0, invalid=762
0301: dt=44.800000, rms=0.503 (0.088%), neg=0, invalid=762
0302: dt=25.600000, rms=0.503 (0.049%), neg=0, invalid=762
0303: dt=25.600000, rms=0.502 (0.065%), neg=0, invalid=762
0304: dt=25.600000, rms=0.502 (0.089%), neg=0, invalid=762
0305: dt=25.600000, rms=0.501 (0.122%), neg=0, invalid=762
0306: dt=25.600000, rms=0.500 (0.140%), neg=0, invalid=762
0307: dt=25.600000, rms=0.500 (0.174%), neg=0, invalid=762
0308: dt=25.600000, rms=0.499 (0.200%), neg=0, invalid=762
0309: dt=25.600000, rms=0.498 (0.187%), neg=0, invalid=762
0310: dt=25.600000, rms=0.497 (0.190%), neg=0, invalid=762
0311: dt=25.600000, rms=0.496 (0.172%), neg=0, invalid=762
0312: dt=25.600000, rms=0.495 (0.191%), neg=0, invalid=762
0313: dt=25.600000, rms=0.494 (0.175%), neg=0, invalid=762
0314: dt=25.600000, rms=0.493 (0.165%), neg=0, invalid=762
0315: dt=25.600000, rms=0.493 (0.130%), neg=0, invalid=762
0316: dt=25.600000, rms=0.492 (0.131%), neg=0, invalid=762
0317: dt=25.600000, rms=0.491 (0.138%), neg=0, invalid=762
0318: dt=25.600000, rms=0.491 (0.124%), neg=0, invalid=762
0319: dt=25.600000, rms=0.491 (0.013%), neg=0, invalid=762
0320: dt=25.600000, rms=0.491 (0.004%), neg=0, invalid=762
0321: dt=25.600000, rms=0.490 (0.024%), neg=0, invalid=762
0322: dt=11.200000, rms=0.490 (0.006%), neg=0, invalid=762
0323: dt=11.200000, rms=0.490 (0.002%), neg=0, invalid=762
0324: dt=11.200000, rms=0.490 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.507, neg=0, invalid=762
0325: dt=0.000000, rms=0.506 (0.041%), neg=0, invalid=762
0326: dt=0.000000, rms=0.506 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.507, neg=0, invalid=762
0327: dt=0.000000, rms=0.506 (0.041%), neg=0, invalid=762
0328: dt=0.000000, rms=0.506 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.539, neg=0, invalid=762
0329: dt=1.280000, rms=0.536 (0.497%), neg=0, invalid=762
0330: dt=0.112000, rms=0.536 (0.006%), neg=0, invalid=762
0331: dt=0.112000, rms=0.536 (0.001%), neg=0, invalid=762
0332: dt=0.112000, rms=0.536 (-0.007%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.537, neg=0, invalid=762
0333: dt=0.768000, rms=0.536 (0.131%), neg=0, invalid=762
0334: dt=0.256000, rms=0.536 (0.006%), neg=0, invalid=762
0335: dt=0.256000, rms=0.536 (-0.001%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.499, neg=0, invalid=762
0336: dt=0.448000, rms=0.486 (2.615%), neg=0, invalid=762
0337: dt=0.448000, rms=0.484 (0.489%), neg=0, invalid=762
0338: dt=0.448000, rms=0.482 (0.287%), neg=0, invalid=762
0339: dt=0.531250, rms=0.481 (0.196%), neg=0, invalid=762
0340: dt=0.448000, rms=0.481 (0.115%), neg=0, invalid=762
0341: dt=0.448000, rms=0.480 (0.080%), neg=0, invalid=762
0342: dt=0.448000, rms=0.480 (0.070%), neg=0, invalid=762
0343: dt=0.448000, rms=0.480 (0.044%), neg=0, invalid=762
0344: dt=0.448000, rms=0.480 (0.046%), neg=0, invalid=762
0345: dt=0.448000, rms=0.479 (0.067%), neg=0, invalid=762
0346: dt=0.448000, rms=0.479 (0.087%), neg=0, invalid=762
0347: dt=0.448000, rms=0.479 (0.075%), neg=0, invalid=762
0348: dt=0.448000, rms=0.479 (0.002%), neg=0, invalid=762
0349: dt=0.448000, rms=0.479 (-0.005%), neg=0, invalid=762
0350: dt=0.112000, rms=0.479 (0.001%), neg=0, invalid=762
0351: dt=0.256000, rms=0.479 (0.001%), neg=0, invalid=762
0352: dt=0.320000, rms=0.479 (0.003%), neg=0, invalid=762
0353: dt=0.192000, rms=0.479 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.479, neg=0, invalid=762
0354: dt=0.448000, rms=0.474 (0.956%), neg=0, invalid=762
0355: dt=0.448000, rms=0.474 (0.136%), neg=0, invalid=762
0356: dt=0.448000, rms=0.473 (0.053%), neg=0, invalid=762
0357: dt=0.448000, rms=0.473 (0.021%), neg=0, invalid=762
0358: dt=0.448000, rms=0.473 (0.008%), neg=0, invalid=762
0359: dt=0.448000, rms=0.473 (0.021%), neg=0, invalid=762
0360: dt=0.448000, rms=0.473 (0.013%), neg=0, invalid=762
0361: dt=0.448000, rms=0.473 (0.016%), neg=0, invalid=762
0362: dt=0.448000, rms=0.473 (0.006%), neg=0, invalid=762
0363: dt=0.320000, rms=0.473 (0.007%), neg=0, invalid=762
0364: dt=0.448000, rms=0.473 (0.005%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
********************* ALLOWING NEGATIVE NODES IN DEFORMATION********************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.471, neg=0, invalid=762
0365: dt=0.000000, rms=0.471 (0.059%), neg=0, invalid=762
0366: dt=0.000000, rms=0.471 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.471, neg=0, invalid=762
0367: dt=129.472000, rms=0.471 (0.088%), neg=0, invalid=762
0368: dt=129.472000, rms=0.471 (0.019%), neg=0, invalid=762
0369: dt=129.472000, rms=0.471 (0.006%), neg=0, invalid=762
0370: dt=129.472000, rms=0.471 (0.027%), neg=0, invalid=762
0371: dt=129.472000, rms=0.470 (0.029%), neg=0, invalid=762
0372: dt=129.472000, rms=0.470 (0.021%), neg=0, invalid=762
0373: dt=129.472000, rms=0.470 (0.009%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.471, neg=0, invalid=762
0374: dt=5.184000, rms=0.470 (0.057%), neg=0, invalid=762
0375: dt=1.307692, rms=0.470 (0.000%), neg=0, invalid=762
0376: dt=1.307692, rms=0.470 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.471, neg=0, invalid=762
0377: dt=145.152000, rms=0.469 (0.344%), neg=0, invalid=762
0378: dt=36.288000, rms=0.469 (0.064%), neg=0, invalid=762
0379: dt=36.288000, rms=0.468 (0.046%), neg=0, invalid=762
0380: dt=36.288000, rms=0.468 (0.066%), neg=0, invalid=762
0381: dt=36.288000, rms=0.468 (0.092%), neg=0, invalid=762
0382: dt=36.288000, rms=0.467 (0.100%), neg=0, invalid=762
0383: dt=36.288000, rms=0.467 (0.104%), neg=0, invalid=762
0384: dt=36.288000, rms=0.466 (0.093%), neg=0, invalid=762
0385: dt=36.288000, rms=0.466 (0.081%), neg=0, invalid=762
0386: dt=145.152000, rms=0.466 (0.026%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.466, neg=0, invalid=762
0387: dt=19.200000, rms=0.465 (0.236%), neg=0, invalid=762
0388: dt=25.600000, rms=0.465 (0.118%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0389: dt=25.600000, rms=0.464 (0.125%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 3 iterations, nbhd size=0, neg = 0
0390: dt=25.600000, rms=0.464 (0.114%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 2 iterations, nbhd size=0, neg = 0
0391: dt=25.600000, rms=0.463 (0.052%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.464, neg=0, invalid=762
0392: dt=60.059701, rms=0.457 (1.497%), neg=0, invalid=762
0393: dt=25.600000, rms=0.455 (0.351%), neg=0, invalid=762
0394: dt=44.800000, rms=0.454 (0.214%), neg=0, invalid=762
0395: dt=44.800000, rms=0.454 (0.117%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0396: dt=44.800000, rms=0.452 (0.309%), neg=0, invalid=762
0397: dt=44.800000, rms=0.451 (0.203%), neg=0, invalid=762
0398: dt=44.800000, rms=0.450 (0.285%), neg=0, invalid=762
0399: dt=44.800000, rms=0.449 (0.290%), neg=0, invalid=762
0400: dt=44.800000, rms=0.448 (0.241%), neg=0, invalid=762
0401: dt=44.800000, rms=0.446 (0.316%), neg=0, invalid=762
0402: dt=44.800000, rms=0.446 (0.103%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
0403: dt=44.800000, rms=0.444 (0.268%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0404: dt=44.800000, rms=0.444 (0.078%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0405: dt=44.800000, rms=0.443 (0.212%), neg=0, invalid=762
0406: dt=44.800000, rms=0.443 (-0.025%), neg=0, invalid=762
0407: dt=19.200000, rms=0.443 (0.064%), neg=0, invalid=762
0408: dt=25.600000, rms=0.443 (0.021%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.448, neg=0, invalid=762
0409: dt=0.000000, rms=0.447 (0.055%), neg=0, invalid=762
0410: dt=0.000000, rms=0.447 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.448, neg=0, invalid=762
0411: dt=1.008000, rms=0.447 (0.059%), neg=0, invalid=762
0412: dt=0.576000, rms=0.447 (0.002%), neg=0, invalid=762
0413: dt=0.576000, rms=0.447 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.456, neg=0, invalid=762
0414: dt=1.024000, rms=0.455 (0.221%), neg=0, invalid=762
0415: dt=0.256000, rms=0.455 (0.005%), neg=0, invalid=762
0416: dt=0.256000, rms=0.455 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.456, neg=0, invalid=762
0417: dt=1.792000, rms=0.455 (0.258%), neg=0, invalid=762
0418: dt=0.448000, rms=0.454 (0.011%), neg=0, invalid=762
0419: dt=0.448000, rms=0.454 (0.011%), neg=0, invalid=762
0420: dt=0.448000, rms=0.454 (-0.010%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.448, neg=0, invalid=762
iter 0, gcam->neg = 517
after 12 iterations, nbhd size=1, neg = 0
0421: dt=2.168911, rms=0.420 (6.215%), neg=0, invalid=762
0422: dt=0.064000, rms=0.420 (0.034%), neg=0, invalid=762
0423: dt=0.064000, rms=0.420 (-0.040%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.420, neg=0, invalid=762
0424: dt=0.064000, rms=0.420 (0.108%), neg=0, invalid=762
0425: dt=0.004000, rms=0.420 (0.009%), neg=0, invalid=762
0426: dt=0.004000, rms=0.420 (-0.000%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
label assignment complete, 0 changed (0.00%)
***************** morphing with label term set to 0 *******************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.405, neg=0, invalid=762
0427: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.405, neg=0, invalid=762
0428: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.405, neg=0, invalid=762
0429: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.405, neg=0, invalid=762
0430: dt=25.920000, rms=0.405 (0.009%), neg=0, invalid=762
0431: dt=36.288000, rms=0.405 (0.007%), neg=0, invalid=762
0432: dt=36.288000, rms=0.405 (0.011%), neg=0, invalid=762
0433: dt=36.288000, rms=0.405 (0.015%), neg=0, invalid=762
0434: dt=36.288000, rms=0.405 (0.015%), neg=0, invalid=762
0435: dt=36.288000, rms=0.405 (0.016%), neg=0, invalid=762
0436: dt=36.288000, rms=0.405 (0.018%), neg=0, invalid=762
0437: dt=36.288000, rms=0.405 (0.017%), neg=0, invalid=762
0438: dt=36.288000, rms=0.405 (0.016%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.406, neg=0, invalid=762
0439: dt=2.800000, rms=0.406 (0.006%), neg=0, invalid=762
0440: dt=1.200000, rms=0.406 (0.001%), neg=0, invalid=762
0441: dt=1.200000, rms=0.406 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.406, neg=0, invalid=762
0442: dt=128.000000, rms=0.403 (0.708%), neg=0, invalid=762
0443: dt=25.600000, rms=0.402 (0.149%), neg=0, invalid=762
0444: dt=25.600000, rms=0.402 (0.059%), neg=0, invalid=762
0445: dt=25.600000, rms=0.402 (0.069%), neg=0, invalid=762
0446: dt=25.600000, rms=0.401 (0.096%), neg=0, invalid=762
0447: dt=25.600000, rms=0.401 (0.128%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
0448: dt=25.600000, rms=0.400 (0.148%), neg=0, invalid=762
0449: dt=25.600000, rms=0.400 (0.152%), neg=0, invalid=762
0450: dt=25.600000, rms=0.399 (0.123%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0451: dt=25.600000, rms=0.399 (0.100%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 5 iterations, nbhd size=0, neg = 0
0452: dt=44.800000, rms=0.399 (0.012%), neg=0, invalid=762
0453: dt=44.800000, rms=0.399 (0.002%), neg=0, invalid=762
0454: dt=44.800000, rms=0.398 (0.034%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0455: dt=44.800000, rms=0.398 (0.032%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0456: dt=44.800000, rms=0.398 (0.024%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.402, neg=0, invalid=762
0457: dt=0.000176, rms=0.402 (0.000%), neg=0, invalid=762
0458: dt=0.000000, rms=0.402 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.402, neg=0, invalid=762
0459: dt=4.032000, rms=0.402 (0.028%), neg=0, invalid=762
0460: dt=5.500000, rms=0.402 (0.018%), neg=0, invalid=762
0461: dt=5.500000, rms=0.401 (0.017%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0462: dt=5.500000, rms=0.401 (0.007%), neg=0, invalid=762
0463: dt=5.500000, rms=0.401 (-0.005%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.407, neg=0, invalid=762
0464: dt=0.000050, rms=0.407 (0.000%), neg=0, invalid=762
0465: dt=0.000000, rms=0.407 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.407, neg=0, invalid=762
0466: dt=0.000000, rms=0.407 (0.000%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.398, neg=0, invalid=762
iter 0, gcam->neg = 401
after 13 iterations, nbhd size=1, neg = 0
0467: dt=1.309920, rms=0.389 (2.131%), neg=0, invalid=762
0468: dt=0.000020, rms=0.389 (0.000%), neg=0, invalid=762
0469: dt=0.000020, rms=0.389 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.389, neg=0, invalid=762
0470: dt=0.096000, rms=0.389 (0.050%), neg=0, invalid=762
0471: dt=0.064000, rms=0.389 (0.012%), neg=0, invalid=762
0472: dt=0.064000, rms=0.389 (0.004%), neg=0, invalid=762
0473: dt=0.064000, rms=0.389 (-0.026%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 1 hours, 47 minutes and 31 seconds.
mri_ca_register utimesec    6441.044000
mri_ca_register stimesec    8.620000
mri_ca_register ru_maxrss   1340484
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   6022171
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  63448
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    309
mri_ca_register ru_nivcsw   9046
FSRUNTIME@ mri_ca_register  1.7921 hours 1 threads
#--------------------------------------
#@# SubCort Seg Mon Feb 15 19:11:50 EST 2021

 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /airflow/apps/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz 

sysname  Linux
hostname mercury-224.braincode.ca
machine  x86_64

setenv SUBJECTS_DIR /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
cd /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /airflow/apps/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz 


== Number of threads available to mri_ca_label for OpenMP = 1 == 
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
using Gibbs prior factor = 0.500
renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-renormalize_mean 0.500
	-regularize 0.500
reading 1 input volumes
reading classifier array from /airflow/apps/freesurfer/average/RB_all_2016-05-10.vc700.gca
reading input volume from norm.mgz
average std[0] = 7.3
reading transform from transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 7.63
Atlas used for the 3D morph was /airflow/apps/freesurfer/average/RB_all_2016-05-10.vc700.gca
average std = 7.3   using min determinant for regularization = 5.3
0 singular and 0 ill-conditioned covariance matrices regularized
labeling volume...
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.16259 (20)
mri peak = 0.23280 (21)
Left_Lateral_Ventricle (4): linear fit = 1.10 x + 0.0 (1319 voxels, overlap=0.765)
Left_Lateral_Ventricle (4): linear fit = 1.10 x + 0.0 (1319 voxels, peak = 22), gca=21.9
gca peak = 0.17677 (13)
mri peak = 0.17951 (21)
Right_Lateral_Ventricle (43): linear fit = 1.46 x + 0.0 (1445 voxels, overlap=0.313)
Right_Lateral_Ventricle (43): linear fit = 1.46 x + 0.0 (1445 voxels, peak = 19), gca=18.9
gca peak = 0.28129 (95)
mri peak = 0.18159 (102)
Right_Pallidum (52): linear fit = 1.07 x + 0.0 (792 voxels, overlap=0.380)
Right_Pallidum (52): linear fit = 1.07 x + 0.0 (792 voxels, peak = 101), gca=101.2
gca peak = 0.16930 (96)
mri peak = 0.16408 (104)
Left_Pallidum (13): linear fit = 1.10 x + 0.0 (774 voxels, overlap=0.018)
Left_Pallidum (13): linear fit = 1.10 x + 0.0 (774 voxels, peak = 105), gca=105.1
gca peak = 0.24553 (55)
mri peak = 0.10561 (75)
Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (1215 voxels, overlap=0.022)
Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (1215 voxels, peak = 70), gca=70.1
gca peak = 0.30264 (59)
mri peak = 0.12933 (73)
Left_Hippocampus (17): linear fit = 1.27 x + 0.0 (1120 voxels, overlap=0.016)
Left_Hippocampus (17): linear fit = 1.27 x + 0.0 (1120 voxels, peak = 75), gca=75.2
gca peak = 0.07580 (103)
mri peak = 0.14092 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52038 voxels, overlap=0.634)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52038 voxels, peak = 104), gca=103.5
gca peak = 0.07714 (104)
mri peak = 0.12701 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (50195 voxels, overlap=0.611)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (50195 voxels, peak = 104), gca=104.0
gca peak = 0.09712 (58)
mri peak = 0.04585 (74)
Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (37309 voxels, overlap=0.022)
Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (37309 voxels, peak = 75), gca=75.1
gca peak = 0.11620 (58)
mri peak = 0.04574 (72)
Right_Cerebral_Cortex (42): linear fit = 1.26 x + 0.0 (31799 voxels, overlap=0.008)
Right_Cerebral_Cortex (42): linear fit = 1.26 x + 0.0 (31799 voxels, peak = 73), gca=73.4
gca peak = 0.30970 (66)
mri peak = 0.11610 (84)
Right_Caudate (50): linear fit = 1.21 x + 0.0 (1180 voxels, overlap=0.020)
Right_Caudate (50): linear fit = 1.21 x + 0.0 (1180 voxels, peak = 80), gca=79.5
gca peak = 0.15280 (69)
mri peak = 0.13064 (84)
Left_Caudate (11): linear fit = 1.13 x + 0.0 (1041 voxels, overlap=0.081)
Left_Caudate (11): linear fit = 1.13 x + 0.0 (1041 voxels, peak = 78), gca=78.3
gca peak = 0.13902 (56)
mri peak = 0.06567 (74)
Left_Cerebellum_Cortex (8): linear fit = 1.34 x + 0.0 (25250 voxels, overlap=0.002)
Left_Cerebellum_Cortex (8): linear fit = 1.34 x + 0.0 (25250 voxels, peak = 75), gca=74.8
gca peak = 0.14777 (55)
mri peak = 0.06481 (77)
Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (23029 voxels, overlap=0.001)
Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (23029 voxels, peak = 74), gca=74.0
gca peak = 0.16765 (84)
mri peak = 0.14493 (93)
Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (6329 voxels, overlap=0.009)
Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (6329 voxels, peak = 92), gca=92.0
gca peak = 0.18739 (84)
mri peak = 0.13225 (93)
Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (9433 voxels, overlap=0.038)
Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (9433 voxels, peak = 92), gca=92.0
gca peak = 0.29869 (57)
mri peak = 0.10779 (74)
Left_Amygdala (18): linear fit = 1.29 x + 0.0 (601 voxels, overlap=0.049)
Left_Amygdala (18): linear fit = 1.29 x + 0.0 (601 voxels, peak = 74), gca=73.8
gca peak = 0.33601 (57)
mri peak = 0.12334 (70)
Right_Amygdala (54): linear fit = 1.24 x + 0.0 (526 voxels, overlap=0.039)
Right_Amygdala (54): linear fit = 1.24 x + 0.0 (526 voxels, peak = 70), gca=70.4
gca peak = 0.11131 (90)
mri peak = 0.08066 (96)
Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (5356 voxels, overlap=0.619)
Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (5356 voxels, peak = 98), gca=97.7
gca peak = 0.11793 (83)
mri peak = 0.09163 (92)
Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5154 voxels, overlap=0.259)
Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5154 voxels, peak = 93), gca=92.5
gca peak = 0.08324 (81)
mri peak = 0.09509 (94)
Left_Putamen (12): linear fit = 1.17 x + 0.0 (1926 voxels, overlap=0.158)
Left_Putamen (12): linear fit = 1.17 x + 0.0 (1926 voxels, peak = 95), gca=95.2
gca peak = 0.10360 (77)
mri peak = 0.07758 (90)
Right_Putamen (51): linear fit = 1.13 x + 0.0 (1985 voxels, overlap=0.364)
Right_Putamen (51): linear fit = 1.13 x + 0.0 (1985 voxels, peak = 87), gca=87.4
gca peak = 0.08424 (78)
mri peak = 0.08482 (88)
Brain_Stem (16): linear fit = 1.13 x + 0.0 (13414 voxels, overlap=0.221)
Brain_Stem (16): linear fit = 1.13 x + 0.0 (13414 voxels, peak = 89), gca=88.5
gca peak = 0.12631 (89)
mri peak = 0.10793 (99)
Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1651 voxels, overlap=0.084)
Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1651 voxels, peak = 100), gca=100.1
gca peak = 0.14500 (87)
mri peak = 0.12128 (101)
Left_VentralDC (28): linear fit = 1.13 x + 0.0 (1692 voxels, overlap=0.163)
Left_VentralDC (28): linear fit = 1.13 x + 0.0 (1692 voxels, peak = 99), gca=98.7
gca peak = 0.14975 (24)
mri peak = 0.11118 (20)
gca peak = 0.19357 (14)
mri peak = 0.16268 (23)
Fourth_Ventricle (15): linear fit = 1.47 x + 0.0 (571 voxels, overlap=0.280)
Fourth_Ventricle (15): linear fit = 1.47 x + 0.0 (571 voxels, peak = 21), gca=20.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Third_Ventricle = 0.14975 (24)
gca peak CSF = 0.23379 (36)
gca peak Left_Accumbens_area = 0.70037 (62)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.24655 (23)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65475 (32)
gca peak WM_hypointensities = 0.07854 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.71127 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.27 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.34 x + 0.0
Left_Putamen too bright - rescaling by 0.981 (from 1.175) to 93.4 (was 95.2)
Left_Pallidum too bright - rescaling by 0.957 (from 1.095) to 100.6 (was 105.1)
Right_Pallidum too bright - rescaling by 0.995 (from 1.065) to 100.6 (was 101.2)
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.16968 (22)
mri peak = 0.23280 (21)
Left_Lateral_Ventricle (4): linear fit = 0.93 x + 0.0 (1319 voxels, overlap=0.793)
Left_Lateral_Ventricle (4): linear fit = 0.93 x + 0.0 (1319 voxels, peak = 20), gca=20.4
gca peak = 0.15941 (18)
mri peak = 0.17951 (21)
Right_Lateral_Ventricle (43): linear fit = 1.09 x + 0.0 (1445 voxels, overlap=0.580)
Right_Lateral_Ventricle (43): linear fit = 1.09 x + 0.0 (1445 voxels, peak = 20), gca=19.5
gca peak = 0.23716 (100)
mri peak = 0.18159 (102)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (792 voxels, overlap=0.999)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (792 voxels, peak = 100), gca=100.5
gca peak = 0.16610 (101)
mri peak = 0.16408 (104)
Left_Pallidum (13): linear fit = 1.04 x + 0.0 (774 voxels, overlap=0.563)
Left_Pallidum (13): linear fit = 1.04 x + 0.0 (774 voxels, peak = 106), gca=105.5
gca peak = 0.24742 (71)
mri peak = 0.10561 (75)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1215 voxels, overlap=1.002)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1215 voxels, peak = 71), gca=71.0
gca peak = 0.25052 (72)
mri peak = 0.12933 (73)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1120 voxels, overlap=1.001)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1120 voxels, peak = 72), gca=72.0
gca peak = 0.07892 (103)
mri peak = 0.14092 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52038 voxels, overlap=0.649)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52038 voxels, peak = 103), gca=103.0
gca peak = 0.07714 (104)
mri peak = 0.12701 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (50195 voxels, overlap=0.611)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (50195 voxels, peak = 104), gca=104.0
gca peak = 0.07486 (75)
mri peak = 0.04585 (74)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (37309 voxels, overlap=0.956)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (37309 voxels, peak = 74), gca=73.9
gca peak = 0.09320 (73)
mri peak = 0.04574 (72)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (31799 voxels, overlap=0.949)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (31799 voxels, peak = 72), gca=71.9
gca peak = 0.22219 (80)
mri peak = 0.11610 (84)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1180 voxels, overlap=1.001)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1180 voxels, peak = 80), gca=80.0
gca peak = 0.14928 (88)
mri peak = 0.13064 (84)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1041 voxels, overlap=0.953)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1041 voxels, peak = 88), gca=88.0
gca peak = 0.10636 (74)
mri peak = 0.06567 (74)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (25250 voxels, overlap=0.975)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (25250 voxels, peak = 74), gca=74.0
gca peak = 0.11229 (74)
mri peak = 0.06481 (77)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (23029 voxels, overlap=0.967)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (23029 voxels, peak = 74), gca=74.0
gca peak = 0.15232 (92)
mri peak = 0.14493 (93)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6329 voxels, overlap=0.836)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6329 voxels, peak = 93), gca=93.4
gca peak = 0.17310 (92)
mri peak = 0.13225 (93)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (9433 voxels, overlap=0.840)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (9433 voxels, peak = 92), gca=91.5
gca peak = 0.29166 (75)
mri peak = 0.10779 (74)
Left_Amygdala (18): linear fit = 0.99 x + 0.0 (601 voxels, overlap=1.004)
Left_Amygdala (18): linear fit = 0.99 x + 0.0 (601 voxels, peak = 74), gca=73.9
gca peak = 0.31442 (70)
mri peak = 0.12334 (70)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (526 voxels, overlap=0.997)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (526 voxels, peak = 70), gca=70.0
gca peak = 0.09760 (97)
mri peak = 0.08066 (96)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5356 voxels, overlap=0.940)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (5356 voxels, peak = 98), gca=98.5
gca peak = 0.10779 (90)
mri peak = 0.09163 (92)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (5154 voxels, overlap=0.854)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (5154 voxels, peak = 91), gca=91.3
gca peak = 0.07248 (92)
mri peak = 0.09509 (94)
Left_Putamen (12): linear fit = 1.02 x + 0.0 (1926 voxels, overlap=0.817)
Left_Putamen (12): linear fit = 1.02 x + 0.0 (1926 voxels, peak = 94), gca=94.3
gca peak = 0.07997 (86)
mri peak = 0.07758 (90)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1985 voxels, overlap=0.941)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1985 voxels, peak = 86), gca=85.6
gca peak = 0.07581 (89)
mri peak = 0.08482 (88)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (13414 voxels, overlap=0.747)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (13414 voxels, peak = 89), gca=89.0
gca peak = 0.10032 (99)
mri peak = 0.10793 (99)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1651 voxels, overlap=0.802)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1651 voxels, peak = 99), gca=99.0
gca peak = 0.15819 (97)
mri peak = 0.12128 (101)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1692 voxels, overlap=0.862)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1692 voxels, peak = 97), gca=96.5
gca peak = 0.14014 (32)
mri peak = 0.11118 (20)
gca peak = 0.14735 (22)
mri peak = 0.16268 (23)
Fourth_Ventricle (15): linear fit = 0.94 x + 0.0 (571 voxels, overlap=0.694)
Fourth_Ventricle (15): linear fit = 0.94 x + 0.0 (571 voxels, peak = 21), gca=20.6
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16048 (41)
gca peak Left_Thalamus = 0.36646 (102)
gca peak Third_Ventricle = 0.14014 (32)
gca peak CSF = 0.17638 (49)
gca peak Left_Accumbens_area = 0.59635 (71)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.11914 (35)
gca peak Right_Inf_Lat_Vent = 0.19636 (29)
gca peak Right_Accumbens_area = 0.29893 (78)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14556 (37)
gca peak Fifth_Ventricle = 0.86987 (42)
gca peak WM_hypointensities = 0.08674 (77)
gca peak non_WM_hypointensities = 0.07427 (44)
gca peak Optic_Chiasm = 0.49920 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 0.99 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 0.98 x + 0.0
Left_Putamen too bright - rescaling by 0.988 (from 1.025) to 93.2 (was 94.3)
Left_Pallidum too bright - rescaling by 0.951 (from 1.045) to 100.4 (was 105.5)
Right_Pallidum too bright - rescaling by 0.999 (from 1.005) to 100.4 (was 100.5)
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt
67655 voxels changed in iteration 0 of unlikely voxel relabeling
353 voxels changed in iteration 1 of unlikely voxel relabeling
8 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
69609 gm and wm labels changed (%29 to gray, %71 to white out of all changed labels)
277 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 70884 changed. image ll: -2.124, PF=0.500
pass 2: 18214 changed. image ll: -2.123, PF=0.500
pass 3: 5094 changed.
pass 4: 1713 changed.
62065 voxels changed in iteration 0 of unlikely voxel relabeling
345 voxels changed in iteration 1 of unlikely voxel relabeling
45 voxels changed in iteration 2 of unlikely voxel relabeling
5 voxels changed in iteration 3 of unlikely voxel relabeling
3 voxels changed in iteration 4 of unlikely voxel relabeling
8887 voxels changed in iteration 0 of unlikely voxel relabeling
144 voxels changed in iteration 1 of unlikely voxel relabeling
14 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
6738 voxels changed in iteration 0 of unlikely voxel relabeling
109 voxels changed in iteration 1 of unlikely voxel relabeling
3 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
5735 voxels changed in iteration 0 of unlikely voxel relabeling
44 voxels changed in iteration 1 of unlikely voxel relabeling
1 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    3026.000000
mri_ca_label stimesec    1.616000
mri_ca_label ru_maxrss   2099296
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   759662
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  0
mri_ca_label ru_oublock  496
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    38
mri_ca_label ru_nivcsw   6165
auto-labeling took 50 minutes and 28 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/transforms/cc_up.lta stripped 

will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/transforms/cc_up.lta
reading aseg from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/aseg.auto_noCCseg.mgz
reading norm from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/norm.mgz
60106 voxels in left wm, 60804 in right wm, xrange [119, 131]
searching rotation angles z=[-2 12], y=[-10  4]
searching scale 1 Z rot -2.3  searching scale 1 Z rot -2.0  searching scale 1 Z rot -1.8  searching scale 1 Z rot -1.5  searching scale 1 Z rot -1.3  searching scale 1 Z rot -1.0  searching scale 1 Z rot -0.8  searching scale 1 Z rot -0.5  searching scale 1 Z rot -0.3  searching scale 1 Z rot -0.0  searching scale 1 Z rot 0.2  searching scale 1 Z rot 0.5  searching scale 1 Z rot 0.7  searching scale 1 Z rot 1.0  searching scale 1 Z rot 1.2  searching scale 1 Z rot 1.5  searching scale 1 Z rot 1.7  searching scale 1 Z rot 2.0  searching scale 1 Z rot 2.2  searching scale 1 Z rot 2.5  searching scale 1 Z rot 2.7  searching scale 1 Z rot 3.0  searching scale 1 Z rot 3.2  searching scale 1 Z rot 3.5  searching scale 1 Z rot 3.7  searching scale 1 Z rot 4.0  searching scale 1 Z rot 4.2  searching scale 1 Z rot 4.5  searching scale 1 Z rot 4.7  searching scale 1 Z rot 5.0  searching scale 1 Z rot 5.2  searching scale 1 Z rot 5.5  searching scale 1 Z rot 5.7  searching scale 1 Z rot 6.0  searching scale 1 Z rot 6.2  searching scale 1 Z rot 6.5  searching scale 1 Z rot 6.7  searching scale 1 Z rot 7.0  searching scale 1 Z rot 7.2  searching scale 1 Z rot 7.5  searching scale 1 Z rot 7.7  searching scale 1 Z rot 8.0  searching scale 1 Z rot 8.2  searching scale 1 Z rot 8.5  searching scale 1 Z rot 8.7  searching scale 1 Z rot 9.0  searching scale 1 Z rot 9.2  searching scale 1 Z rot 9.5  searching scale 1 Z rot 9.7  searching scale 1 Z rot 10.0  searching scale 1 Z rot 10.2  searching scale 1 Z rot 10.5  searching scale 1 Z rot 10.7  searching scale 1 Z rot 11.0  searching scale 1 Z rot 11.2  searching scale 1 Z rot 11.5  global minimum found at slice 124.4, rotations (-2.70, 4.72)
final transformation (x=124.4, yr=-2.696, zr=4.724):
 0.99550  -0.08235  -0.04687   15.87933;
 0.08226   0.99660  -0.00387   40.46899;
 0.04703   0.00000   0.99889   10.27552;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [126, 130] in xformed coordinates
best xformed slice 127
cc center is found at 127 78 112
eigenvectors:
 0.00033   0.00222   1.00000;
-0.08522  -0.99636   0.00224;
 0.99636  -0.08522  -0.00014;
error in mid anterior detected - correcting...
writing aseg with callosum to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/aseg.auto.mgz...
corpus callosum segmentation took 0.9 minutes
#--------------------------------------
#@# Merge ASeg Mon Feb 15 20:03:10 EST 2021

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Mon Feb 15 20:03:10 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri

 mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz 

assuming input volume is MGH (Van der Kouwe) MP-RAGE
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading from norm.mgz...
Reading aseg aseg.presurf.mgz
normalizing image...
processing with aseg
removing outliers in the aseg WM...
681 control points removed
Building bias image
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
Smoothing with sigma 8
Applying bias correction
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 80 (80), valley at 33 (33)
csf peak at 40, setting threshold to 66
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 79 (79), valley at 32 (32)
csf peak at 40, setting threshold to 66
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 2 minutes and 44 seconds.
#--------------------------------------------
#@# Mask BFS Mon Feb 15 20:05:55 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5
DoAbs = 0
Found 1699047 voxels in mask (pct= 10.13)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Mon Feb 15 20:05:57 EST 2021

 mri_segment -mprage brain.mgz wm.seg.mgz 

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (103.0): 102.7 +- 6.6 [79.0 --> 125.0]
GM (76.0) : 75.3 +- 10.3 [30.0 --> 95.0]
setting bottom of white matter range to 85.6
setting top of gray matter range to 95.9
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...

reclassifying voxels using Gaussian border classifier...

removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
4357 sparsely connected voxels removed...
thickening thin strands....
20 segments, 3460 filled
95 bright non-wm voxels segmented.
2786 diagonally connected voxels added...
white matter segmentation took 1.4 minutes
writing output to wm.seg.mgz...
assuming input volume is MGH (Van der Kouwe) MP-RAGE

 mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz 

preserving editing changes in input volume...
auto filling took 0.37 minutes
reading wm segmentation from wm.seg.mgz...
15 voxels added to wm to prevent paths from MTL structures to cortex
3399 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 38670 voxels turned on, 62729 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 0   new 0
115,126,128 old 0   new 0
writing edited volume to wm.asegedit.mgz....

 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz 


Iteration Number : 1
pass   1 (xy+):  22 found -  22 modified     |    TOTAL:  22
pass   2 (xy+):   0 found -  22 modified     |    TOTAL:  22
pass   1 (xy-):  20 found -  20 modified     |    TOTAL:  42
pass   2 (xy-):   0 found -  20 modified     |    TOTAL:  42
pass   1 (yz+):  13 found -  13 modified     |    TOTAL:  55
pass   2 (yz+):   0 found -  13 modified     |    TOTAL:  55
pass   1 (yz-):  23 found -  23 modified     |    TOTAL:  78
pass   2 (yz-):   0 found -  23 modified     |    TOTAL:  78
pass   1 (xz+):   9 found -   9 modified     |    TOTAL:  87
pass   2 (xz+):   0 found -   9 modified     |    TOTAL:  87
pass   1 (xz-):  13 found -  13 modified     |    TOTAL: 100
pass   2 (xz-):   0 found -  13 modified     |    TOTAL: 100
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   3 found -   3 modified     |    TOTAL:   3
pass   2 (+++):   0 found -   3 modified     |    TOTAL:   3
pass   1 (+++):   4 found -   4 modified     |    TOTAL:   7
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   7
pass   1 (+++):   4 found -   4 modified     |    TOTAL:  11
pass   2 (+++):   0 found -   4 modified     |    TOTAL:  11
Iteration Number : 1
pass   1 (++):  69 found -  69 modified     |    TOTAL:  69
pass   2 (++):   0 found -  69 modified     |    TOTAL:  69
pass   1 (+-):  56 found -  56 modified     |    TOTAL: 125
pass   2 (+-):   0 found -  56 modified     |    TOTAL: 125
pass   1 (--):  86 found -  86 modified     |    TOTAL: 211
pass   2 (--):   0 found -  86 modified     |    TOTAL: 211
pass   1 (-+):  87 found -  87 modified     |    TOTAL: 298
pass   2 (-+):   0 found -  87 modified     |    TOTAL: 298
Iteration Number : 2
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   3 found -   3 modified     |    TOTAL:   5
pass   2 (xy-):   0 found -   3 modified     |    TOTAL:   5
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   6
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   6
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   7
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   7
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   7
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   8
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   8
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (--):   0 found -   0 modified     |    TOTAL:   2
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 419 (out of 616907: 0.067919)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Mon Feb 15 20:07:48 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri

 mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.auto_noCCseg.mgz...
reading input volume...done.
searching for cutting planes...voxel to talairach voxel transform
 1.09088  -0.09213  -0.04692   3.68430;
 0.09898   0.94672   0.23376  -12.66487;
 0.01134  -0.27152   0.93811   25.33225;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.09088  -0.09213  -0.04692   3.68430;
 0.09898   0.94672   0.23376  -12.66487;
 0.01134  -0.27152   0.93811   25.33225;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1223 (min = 350, max = 1400), aspect = 0.42 (min = 0.10, max = 0.75)
no need to search
using seed (126, 123, 150), TAL = (2.0, 22.0, 5.0)
talairach voxel to voxel transform
 0.90788   0.09461   0.02183  -2.69965;
-0.08606   0.97686  -0.24771   18.96399;
-0.03588   0.28159   0.99401  -21.48212;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (126,  123,  150) --> (2.0, 22.0, 5.0)
done.
writing output to filled.mgz...
filling took 0.5 minutes
talairach cc position changed to (2.00, 22.00, 5.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(20.00, 22.00, 5.00) SRC: (110.26, 92.67, 158.38)
search lh wm seed point around talairach space (-16.00, 22.00, 5.00), SRC: (142.95, 89.57, 157.09)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Mon Feb 15 20:08:19 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz 


Iteration Number : 1
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (yz+):   4 found -   4 modified     |    TOTAL:   6
pass   2 (yz+):   0 found -   4 modified     |    TOTAL:   6
pass   1 (yz-):   4 found -   4 modified     |    TOTAL:  10
pass   2 (yz-):   0 found -   4 modified     |    TOTAL:  10
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:  10
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:  11
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:  11
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   2 found -   2 modified     |    TOTAL:   2
pass   2 (--):   0 found -   2 modified     |    TOTAL:   2
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   3
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   3
Iteration Number : 2
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   2
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   1
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 17 (out of 295009: 0.005763)
Ambiguous edge configurations... 

mri_pretess done


 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 40: 1055 vertices, 1167 faces
slice 50: 6515 vertices, 6786 faces
slice 60: 15996 vertices, 16352 faces
slice 70: 26807 vertices, 27226 faces
slice 80: 38604 vertices, 38982 faces
slice 90: 50650 vertices, 51083 faces
slice 100: 63340 vertices, 63769 faces
slice 110: 75750 vertices, 76173 faces
slice 120: 87635 vertices, 88082 faces
slice 130: 99455 vertices, 99872 faces
slice 140: 110125 vertices, 110516 faces
slice 150: 119769 vertices, 120110 faces
slice 160: 127726 vertices, 128042 faces
slice 170: 135263 vertices, 135552 faces
slice 180: 141361 vertices, 141615 faces
slice 190: 146722 vertices, 146910 faces
slice 200: 149601 vertices, 149688 faces
slice 210: 149874 vertices, 149914 faces
slice 220: 149874 vertices, 149914 faces
slice 230: 149874 vertices, 149914 faces
slice 240: 149874 vertices, 149914 faces
slice 250: 149874 vertices, 149914 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   149874 voxel in cpt #1: X=-40 [v=149874,e=449742,f=299828] located at (-23.285339, -17.193716, 40.630398)
For the whole surface: X=-40 [v=149874,e=449742,f=299828]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Mon Feb 15 20:08:24 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 3 (out of 301013: 0.000997)
Ambiguous edge configurations... 

mri_pretess done


 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 40: 984 vertices, 1100 faces
slice 50: 6797 vertices, 7053 faces
slice 60: 15710 vertices, 16058 faces
slice 70: 26522 vertices, 26941 faces
slice 80: 38654 vertices, 39038 faces
slice 90: 49678 vertices, 50027 faces
slice 100: 61864 vertices, 62300 faces
slice 110: 74211 vertices, 74631 faces
slice 120: 86509 vertices, 86951 faces
slice 130: 98683 vertices, 99100 faces
slice 140: 109311 vertices, 109717 faces
slice 150: 119458 vertices, 119774 faces
slice 160: 127904 vertices, 128210 faces
slice 170: 135200 vertices, 135462 faces
slice 180: 142165 vertices, 142406 faces
slice 190: 147928 vertices, 148130 faces
slice 200: 151843 vertices, 151978 faces
slice 210: 152592 vertices, 152618 faces
slice 220: 152592 vertices, 152618 faces
slice 230: 152592 vertices, 152618 faces
slice 240: 152592 vertices, 152618 faces
slice 250: 152592 vertices, 152618 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   152592 voxel in cpt #1: X=-26 [v=152592,e=457854,f=305236] located at (29.816366, -15.322697, 36.758003)
For the whole surface: X=-26 [v=152592,e=457854,f=305236]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Mon Feb 15 20:08:29 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Smooth1 rh Mon Feb 15 20:08:33 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Inflation1 lh Mon Feb 15 20:08:38 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 48.5 mm, total surface area = 79591 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.5 minutes
step 000: RMS=0.153 (target=0.015)   step 005: RMS=0.114 (target=0.015)   step 010: RMS=0.084 (target=0.015)   step 015: RMS=0.069 (target=0.015)   step 020: RMS=0.059 (target=0.015)   step 025: RMS=0.050 (target=0.015)   step 030: RMS=0.044 (target=0.015)   step 035: RMS=0.040 (target=0.015)   step 040: RMS=0.038 (target=0.015)   step 045: RMS=0.036 (target=0.015)   step 050: RMS=0.035 (target=0.015)   step 055: RMS=0.034 (target=0.015)   step 060: RMS=0.033 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    28.052000
mris_inflate stimesec    0.148000
mris_inflate ru_maxrss   197108
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   47694
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  10544
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    50
mris_inflate ru_nivcsw   321
#--------------------------------------------
#@# Inflation1 rh Mon Feb 15 20:09:06 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 49.1 mm, total surface area = 81010 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.5 minutes
step 000: RMS=0.151 (target=0.015)   step 005: RMS=0.113 (target=0.015)   step 010: RMS=0.082 (target=0.015)   step 015: RMS=0.068 (target=0.015)   step 020: RMS=0.057 (target=0.015)   step 025: RMS=0.049 (target=0.015)   step 030: RMS=0.043 (target=0.015)   step 035: RMS=0.039 (target=0.015)   step 040: RMS=0.036 (target=0.015)   step 045: RMS=0.035 (target=0.015)   step 050: RMS=0.034 (target=0.015)   step 055: RMS=0.033 (target=0.015)   step 060: RMS=0.032 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    28.476000
mris_inflate stimesec    0.100000
mris_inflate ru_maxrss   200464
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   48567
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  10736
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    58
mris_inflate ru_nivcsw   46
#--------------------------------------------
#@# QSphere lh Mon Feb 15 20:09:35 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix 

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.95 +- 0.55 (0.00-->6.14) (max @ vno 111821 --> 111852)
face area 0.02 +- 0.03 (-0.16-->0.56)

== Number of threads available to mris_sphere for OpenMP = 1 == 
scaling brain by 0.301...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.554, avgs=0
005/300: dt: 0.9000, rms radial error=176.294, avgs=0
010/300: dt: 0.9000, rms radial error=175.737, avgs=0
015/300: dt: 0.9000, rms radial error=175.006, avgs=0
020/300: dt: 0.9000, rms radial error=174.172, avgs=0
025/300: dt: 0.9000, rms radial error=173.281, avgs=0
030/300: dt: 0.9000, rms radial error=172.358, avgs=0
035/300: dt: 0.9000, rms radial error=171.419, avgs=0
040/300: dt: 0.9000, rms radial error=170.472, avgs=0
045/300: dt: 0.9000, rms radial error=169.524, avgs=0
050/300: dt: 0.9000, rms radial error=168.576, avgs=0
055/300: dt: 0.9000, rms radial error=167.630, avgs=0
060/300: dt: 0.9000, rms radial error=166.689, avgs=0
065/300: dt: 0.9000, rms radial error=165.751, avgs=0
070/300: dt: 0.9000, rms radial error=164.818, avgs=0
075/300: dt: 0.9000, rms radial error=163.890, avgs=0
080/300: dt: 0.9000, rms radial error=162.967, avgs=0
085/300: dt: 0.9000, rms radial error=162.048, avgs=0
090/300: dt: 0.9000, rms radial error=161.135, avgs=0
095/300: dt: 0.9000, rms radial error=160.226, avgs=0
100/300: dt: 0.9000, rms radial error=159.322, avgs=0
105/300: dt: 0.9000, rms radial error=158.423, avgs=0
110/300: dt: 0.9000, rms radial error=157.529, avgs=0
115/300: dt: 0.9000, rms radial error=156.640, avgs=0
120/300: dt: 0.9000, rms radial error=155.756, avgs=0
125/300: dt: 0.9000, rms radial error=154.876, avgs=0
130/300: dt: 0.9000, rms radial error=154.001, avgs=0
135/300: dt: 0.9000, rms radial error=153.131, avgs=0
140/300: dt: 0.9000, rms radial error=152.266, avgs=0
145/300: dt: 0.9000, rms radial error=151.405, avgs=0
150/300: dt: 0.9000, rms radial error=150.550, avgs=0
155/300: dt: 0.9000, rms radial error=149.699, avgs=0
160/300: dt: 0.9000, rms radial error=148.853, avgs=0
165/300: dt: 0.9000, rms radial error=148.012, avgs=0
170/300: dt: 0.9000, rms radial error=147.175, avgs=0
175/300: dt: 0.9000, rms radial error=146.343, avgs=0
180/300: dt: 0.9000, rms radial error=145.517, avgs=0
185/300: dt: 0.9000, rms radial error=144.698, avgs=0
190/300: dt: 0.9000, rms radial error=143.883, avgs=0
195/300: dt: 0.9000, rms radial error=143.074, avgs=0
200/300: dt: 0.9000, rms radial error=142.268, avgs=0
205/300: dt: 0.9000, rms radial error=141.467, avgs=0
210/300: dt: 0.9000, rms radial error=140.671, avgs=0
215/300: dt: 0.9000, rms radial error=139.879, avgs=0
220/300: dt: 0.9000, rms radial error=139.092, avgs=0
225/300: dt: 0.9000, rms radial error=138.309, avgs=0
230/300: dt: 0.9000, rms radial error=137.531, avgs=0
235/300: dt: 0.9000, rms radial error=136.757, avgs=0
240/300: dt: 0.9000, rms radial error=135.987, avgs=0
245/300: dt: 0.9000, rms radial error=135.222, avgs=0
250/300: dt: 0.9000, rms radial error=134.460, avgs=0
255/300: dt: 0.9000, rms radial error=133.704, avgs=0
260/300: dt: 0.9000, rms radial error=132.951, avgs=0
265/300: dt: 0.9000, rms radial error=132.203, avgs=0
270/300: dt: 0.9000, rms radial error=131.459, avgs=0
275/300: dt: 0.9000, rms radial error=130.719, avgs=0
280/300: dt: 0.9000, rms radial error=129.983, avgs=0
285/300: dt: 0.9000, rms radial error=129.251, avgs=0
290/300: dt: 0.9000, rms radial error=128.523, avgs=0
295/300: dt: 0.9000, rms radial error=127.799, avgs=0
300/300: dt: 0.9000, rms radial error=127.080, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 17712.49
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00014
epoch 2 (K=40.0), pass 1, starting sse = 3033.30
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00005
epoch 3 (K=160.0), pass 1, starting sse = 314.24
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.09/11 = 0.00855
epoch 4 (K=640.0), pass 1, starting sse = 16.15
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.19/17 = 0.01126
final distance error %27.14
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.05 hours
mris_sphere utimesec    190.172000
mris_sphere stimesec    0.300000
mris_sphere ru_maxrss   197584
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   47706
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10544
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    57
mris_sphere ru_nivcsw   806
FSRUNTIME@ mris_sphere  0.0529 hours 1 threads
#--------------------------------------------
#@# QSphere rh Mon Feb 15 20:12:46 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix 

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.94 +- 0.55 (0.00-->6.68) (max @ vno 79660 --> 80946)
face area 0.02 +- 0.03 (-0.08-->0.42)

== Number of threads available to mris_sphere for OpenMP = 1 == 
scaling brain by 0.295...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.629, avgs=0
005/300: dt: 0.9000, rms radial error=176.370, avgs=0
010/300: dt: 0.9000, rms radial error=175.813, avgs=0
015/300: dt: 0.9000, rms radial error=175.081, avgs=0
020/300: dt: 0.9000, rms radial error=174.248, avgs=0
025/300: dt: 0.9000, rms radial error=173.358, avgs=0
030/300: dt: 0.9000, rms radial error=172.435, avgs=0
035/300: dt: 0.9000, rms radial error=171.497, avgs=0
040/300: dt: 0.9000, rms radial error=170.550, avgs=0
045/300: dt: 0.9000, rms radial error=169.602, avgs=0
050/300: dt: 0.9000, rms radial error=168.654, avgs=0
055/300: dt: 0.9000, rms radial error=167.709, avgs=0
060/300: dt: 0.9000, rms radial error=166.769, avgs=0
065/300: dt: 0.9000, rms radial error=165.833, avgs=0
070/300: dt: 0.9000, rms radial error=164.901, avgs=0
075/300: dt: 0.9000, rms radial error=163.975, avgs=0
080/300: dt: 0.9000, rms radial error=163.053, avgs=0
085/300: dt: 0.9000, rms radial error=162.137, avgs=0
090/300: dt: 0.9000, rms radial error=161.225, avgs=0
095/300: dt: 0.9000, rms radial error=160.319, avgs=0
100/300: dt: 0.9000, rms radial error=159.417, avgs=0
105/300: dt: 0.9000, rms radial error=158.521, avgs=0
110/300: dt: 0.9000, rms radial error=157.630, avgs=0
115/300: dt: 0.9000, rms radial error=156.744, avgs=0
120/300: dt: 0.9000, rms radial error=155.864, avgs=0
125/300: dt: 0.9000, rms radial error=154.991, avgs=0
130/300: dt: 0.9000, rms radial error=154.122, avgs=0
135/300: dt: 0.9000, rms radial error=153.258, avgs=0
140/300: dt: 0.9000, rms radial error=152.399, avgs=0
145/300: dt: 0.9000, rms radial error=151.545, avgs=0
150/300: dt: 0.9000, rms radial error=150.695, avgs=0
155/300: dt: 0.9000, rms radial error=149.849, avgs=0
160/300: dt: 0.9000, rms radial error=149.009, avgs=0
165/300: dt: 0.9000, rms radial error=148.173, avgs=0
170/300: dt: 0.9000, rms radial error=147.342, avgs=0
175/300: dt: 0.9000, rms radial error=146.515, avgs=0
180/300: dt: 0.9000, rms radial error=145.693, avgs=0
185/300: dt: 0.9000, rms radial error=144.876, avgs=0
190/300: dt: 0.9000, rms radial error=144.063, avgs=0
195/300: dt: 0.9000, rms radial error=143.255, avgs=0
200/300: dt: 0.9000, rms radial error=142.451, avgs=0
205/300: dt: 0.9000, rms radial error=141.651, avgs=0
210/300: dt: 0.9000, rms radial error=140.856, avgs=0
215/300: dt: 0.9000, rms radial error=140.066, avgs=0
220/300: dt: 0.9000, rms radial error=139.279, avgs=0
225/300: dt: 0.9000, rms radial error=138.497, avgs=0
230/300: dt: 0.9000, rms radial error=137.719, avgs=0
235/300: dt: 0.9000, rms radial error=136.946, avgs=0
240/300: dt: 0.9000, rms radial error=136.177, avgs=0
245/300: dt: 0.9000, rms radial error=135.412, avgs=0
250/300: dt: 0.9000, rms radial error=134.651, avgs=0
255/300: dt: 0.9000, rms radial error=133.895, avgs=0
260/300: dt: 0.9000, rms radial error=133.143, avgs=0
265/300: dt: 0.9000, rms radial error=132.395, avgs=0
270/300: dt: 0.9000, rms radial error=131.651, avgs=0
275/300: dt: 0.9000, rms radial error=130.911, avgs=0
280/300: dt: 0.9000, rms radial error=130.176, avgs=0
285/300: dt: 0.9000, rms radial error=129.444, avgs=0
290/300: dt: 0.9000, rms radial error=128.717, avgs=0
295/300: dt: 0.9000, rms radial error=127.993, avgs=0
300/300: dt: 0.9000, rms radial error=127.274, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 18118.90
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00018
epoch 2 (K=40.0), pass 1, starting sse = 3109.20
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00008
epoch 3 (K=160.0), pass 1, starting sse = 333.18
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.12/11 = 0.01052
epoch 4 (K=640.0), pass 1, starting sse = 18.65
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.25/18 = 0.01371
final distance error %27.00
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.05 hours
mris_sphere utimesec    195.488000
mris_sphere stimesec    0.116000
mris_sphere ru_maxrss   201368
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   48579
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10736
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    58
mris_sphere ru_nivcsw   1999
FSRUNTIME@ mris_sphere  0.0544 hours 1 threads
#--------------------------------------------
#@# Fix Topology Copy lh Mon Feb 15 20:16:02 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 cp ../surf/lh.orig.nofix ../surf/lh.orig 


 cp ../surf/lh.inflated.nofix ../surf/lh.inflated 

#--------------------------------------------
#@# Fix Topology Copy rh Mon Feb 15 20:16:02 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 cp ../surf/rh.orig.nofix ../surf/rh.orig 


 cp ../surf/rh.inflated.nofix ../surf/rh.inflated 

#@# Fix Topology lh Mon Feb 15 20:16:02 EST 2021

 mris_fix_topology -rusage /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 stripped lh 

reading spherical homeomorphism from 'qsphere.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234

*************************************************************
Topology Correction Parameters
retessellation mode:           genetic search
number of patches/generation : 10
number of generations :        10
surface mri loglikelihood coefficient :         1.0
volume mri loglikelihood coefficient :          10.0
normal dot loglikelihood coefficient :          1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution :                             2
eliminate vertices during search :              1
initial patch selection :                       1
select all defect vertices :                    0
ordering dependant retessellation:              0
use precomputed edge table :                    0
smooth retessellated patch :                    2
match retessellated patch :                     1
verbose mode :                                  0

*************************************************************
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
before topology correction, eno=-40 (nv=149874, nf=299828, ne=449742, g=21)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
marking ambiguous vertices...
2401 ambiguous faces found in tessellation
segmenting defects...
21 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
21 defects to be corrected 
0 vertices coincident
reading input surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.2914  (-4.6457)
      -vertex     loglikelihood: -5.8614  (-2.9307)
      -normal dot loglikelihood: -3.6699  (-3.6699)
      -quad curv  loglikelihood: -5.8710  (-2.9355)
      Total Loglikelihood : -24.6937

CORRECTING DEFECT 0 (vertices=53, convex hull=66, v0=16442)
After retessellation of defect 0 (v0=16442), euler #=-18 (148415,444641,296208) : difference with theory (-18) = 0 

CORRECTING DEFECT 1 (vertices=27, convex hull=61, v0=23665)
After retessellation of defect 1 (v0=23665), euler #=-17 (148431,444714,296266) : difference with theory (-17) = 0 

CORRECTING DEFECT 2 (vertices=35, convex hull=87, v0=49806)
After retessellation of defect 2 (v0=49806), euler #=-16 (148445,444791,296330) : difference with theory (-16) = 0 

CORRECTING DEFECT 3 (vertices=49, convex hull=29, v0=57769)
After retessellation of defect 3 (v0=57769), euler #=-15 (148451,444818,296352) : difference with theory (-15) = 0 

CORRECTING DEFECT 4 (vertices=91, convex hull=79, v0=61628)
After retessellation of defect 4 (v0=61628), euler #=-14 (148478,444926,296434) : difference with theory (-14) = 0 

CORRECTING DEFECT 5 (vertices=145, convex hull=141, v0=64269)
After retessellation of defect 5 (v0=64269), euler #=-13 (148530,445153,296610) : difference with theory (-13) = 0 

CORRECTING DEFECT 6 (vertices=10, convex hull=14, v0=68902)
After retessellation of defect 6 (v0=68902), euler #=-12 (148531,445159,296616) : difference with theory (-12) = 0 

CORRECTING DEFECT 7 (vertices=18, convex hull=27, v0=74198)
After retessellation of defect 7 (v0=74198), euler #=-11 (148533,445173,296629) : difference with theory (-11) = 0 

CORRECTING DEFECT 8 (vertices=99, convex hull=147, v0=79602)
After retessellation of defect 8 (v0=79602), euler #=-10 (148576,445375,296789) : difference with theory (-10) = 0 

CORRECTING DEFECT 9 (vertices=166, convex hull=73, v0=81449)
After retessellation of defect 9 (v0=81449), euler #=-9 (148588,445446,296849) : difference with theory (-9) = 0 

CORRECTING DEFECT 10 (vertices=116, convex hull=46, v0=95755)
After retessellation of defect 10 (v0=95755), euler #=-8 (148599,445498,296891) : difference with theory (-8) = 0 

CORRECTING DEFECT 11 (vertices=21, convex hull=57, v0=102296)
After retessellation of defect 11 (v0=102296), euler #=-7 (148611,445555,296937) : difference with theory (-7) = 0 

CORRECTING DEFECT 12 (vertices=290, convex hull=176, v0=102314)
After retessellation of defect 12 (v0=102314), euler #=-6 (148670,445823,297147) : difference with theory (-6) = 0 

CORRECTING DEFECT 13 (vertices=68, convex hull=84, v0=108953)
After retessellation of defect 13 (v0=108953), euler #=-5 (148699,445948,297244) : difference with theory (-5) = 0 

CORRECTING DEFECT 14 (vertices=146, convex hull=61, v0=109864)
After retessellation of defect 14 (v0=109864), euler #=-4 (148708,446003,297291) : difference with theory (-4) = 0 

CORRECTING DEFECT 15 (vertices=20, convex hull=48, v0=113982)
After retessellation of defect 15 (v0=113982), euler #=-3 (148717,446045,297325) : difference with theory (-3) = 0 

CORRECTING DEFECT 16 (vertices=41, convex hull=69, v0=115218)
After retessellation of defect 16 (v0=115218), euler #=-2 (148731,446116,297383) : difference with theory (-2) = 0 

CORRECTING DEFECT 17 (vertices=16, convex hull=46, v0=117908)
After retessellation of defect 17 (v0=117908), euler #=-1 (148740,446158,297417) : difference with theory (-1) = 0 

CORRECTING DEFECT 18 (vertices=17, convex hull=61, v0=123175)
After retessellation of defect 18 (v0=123175), euler #=0 (148746,446195,297449) : difference with theory (0) = 0 

CORRECTING DEFECT 19 (vertices=39, convex hull=64, v0=124704)
After retessellation of defect 19 (v0=124704), euler #=1 (148760,446263,297504) : difference with theory (1) = 0 

CORRECTING DEFECT 20 (vertices=7, convex hull=27, v0=126915)
After retessellation of defect 20 (v0=126915), euler #=2 (148761,446277,297518) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.13-->7.81) (max @ vno 104673 --> 105743)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.22 (0.13-->7.81) (max @ vno 104673 --> 105743)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
76 mutations (31.4%), 166 crossovers (68.6%), 117 vertices were eliminated
building final representation...
1113 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=148761, nf=297518, ne=446277, g=0)
writing corrected surface to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 10.9 minutes
0 defective edges
removing intersecting faces
000: 162 intersecting
001: 11 intersecting
mris_fix_topology utimesec    652.552000
mris_fix_topology stimesec    0.264000
mris_fix_topology ru_maxrss   473928
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   117475
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  0
mris_fix_topology ru_oublock  13992
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    103
mris_fix_topology ru_nivcsw   2000
FSRUNTIME@ mris_fix_topology lh  0.1814 hours 1 threads
#@# Fix Topology rh Mon Feb 15 20:26:55 EST 2021

 mris_fix_topology -rusage /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 stripped rh 

reading spherical homeomorphism from 'qsphere.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234

*************************************************************
Topology Correction Parameters
retessellation mode:           genetic search
number of patches/generation : 10
number of generations :        10
surface mri loglikelihood coefficient :         1.0
volume mri loglikelihood coefficient :          10.0
normal dot loglikelihood coefficient :          1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution :                             2
eliminate vertices during search :              1
initial patch selection :                       1
select all defect vertices :                    0
ordering dependant retessellation:              0
use precomputed edge table :                    0
smooth retessellated patch :                    2
match retessellated patch :                     1
verbose mode :                                  0

*************************************************************
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
before topology correction, eno=-26 (nv=152592, nf=305236, ne=457854, g=14)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
marking ambiguous vertices...
2226 ambiguous faces found in tessellation
segmenting defects...
26 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 12 into 10
25 defects to be corrected 
0 vertices coincident
reading input surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.3236  (-4.6618)
      -vertex     loglikelihood: -5.8911  (-2.9455)
      -normal dot loglikelihood: -3.6193  (-3.6193)
      -quad curv  loglikelihood: -6.4969  (-3.2484)
      Total Loglikelihood : -25.3308

CORRECTING DEFECT 0 (vertices=103, convex hull=106, v0=308)
After retessellation of defect 0 (v0=308), euler #=-23 (151230,453130,301877) : difference with theory (-22) = 1 

CORRECTING DEFECT 1 (vertices=112, convex hull=109, v0=953)
After retessellation of defect 1 (v0=953), euler #=-22 (151252,453246,301972) : difference with theory (-21) = 1 

CORRECTING DEFECT 2 (vertices=6, convex hull=23, v0=62736)
After retessellation of defect 2 (v0=62736), euler #=-21 (151255,453262,301986) : difference with theory (-20) = 1 

CORRECTING DEFECT 3 (vertices=18, convex hull=23, v0=72630)
After retessellation of defect 3 (v0=72630), euler #=-20 (151257,453277,302000) : difference with theory (-19) = 1 

CORRECTING DEFECT 4 (vertices=15, convex hull=22, v0=75015)
After retessellation of defect 4 (v0=75015), euler #=-19 (151259,453290,302012) : difference with theory (-18) = 1 

CORRECTING DEFECT 5 (vertices=258, convex hull=134, v0=78682)
After retessellation of defect 5 (v0=78682), euler #=-18 (151285,453432,302129) : difference with theory (-17) = 1 

CORRECTING DEFECT 6 (vertices=75, convex hull=54, v0=99521)
After retessellation of defect 6 (v0=99521), euler #=-17 (151291,453473,302165) : difference with theory (-16) = 1 

CORRECTING DEFECT 7 (vertices=6, convex hull=18, v0=100355)
After retessellation of defect 7 (v0=100355), euler #=-16 (151294,453487,302177) : difference with theory (-15) = 1 

CORRECTING DEFECT 8 (vertices=50, convex hull=42, v0=103785)
After retessellation of defect 8 (v0=103785), euler #=-15 (151302,453526,302209) : difference with theory (-14) = 1 

CORRECTING DEFECT 9 (vertices=52, convex hull=69, v0=106848)
After retessellation of defect 9 (v0=106848), euler #=-14 (151322,453613,302277) : difference with theory (-13) = 1 

CORRECTING DEFECT 10 (vertices=212, convex hull=63, v0=108902)
After retessellation of defect 10 (v0=108902), euler #=-12 (151342,453699,302345) : difference with theory (-12) = 0 

CORRECTING DEFECT 11 (vertices=7, convex hull=19, v0=110977)
After retessellation of defect 11 (v0=110977), euler #=-11 (151344,453708,302353) : difference with theory (-11) = 0 

CORRECTING DEFECT 12 (vertices=5, convex hull=29, v0=112453)
After retessellation of defect 12 (v0=112453), euler #=-10 (151346,453721,302365) : difference with theory (-10) = 0 

CORRECTING DEFECT 13 (vertices=36, convex hull=79, v0=112684)
After retessellation of defect 13 (v0=112684), euler #=-9 (151364,453812,302439) : difference with theory (-9) = 0 

CORRECTING DEFECT 14 (vertices=26, convex hull=33, v0=113381)
After retessellation of defect 14 (v0=113381), euler #=-8 (151368,453835,302459) : difference with theory (-8) = 0 

CORRECTING DEFECT 15 (vertices=15, convex hull=30, v0=113473)
After retessellation of defect 15 (v0=113473), euler #=-7 (151369,453848,302472) : difference with theory (-7) = 0 

CORRECTING DEFECT 16 (vertices=75, convex hull=100, v0=123744)
After retessellation of defect 16 (v0=123744), euler #=-6 (151378,453916,302532) : difference with theory (-6) = 0 

CORRECTING DEFECT 17 (vertices=38, convex hull=62, v0=124450)
After retessellation of defect 17 (v0=124450), euler #=-5 (151394,453989,302590) : difference with theory (-5) = 0 

CORRECTING DEFECT 18 (vertices=116, convex hull=99, v0=125251)
After retessellation of defect 18 (v0=125251), euler #=-4 (151429,454143,302710) : difference with theory (-4) = 0 

CORRECTING DEFECT 19 (vertices=22, convex hull=28, v0=130863)
After retessellation of defect 19 (v0=130863), euler #=-3 (151433,454165,302729) : difference with theory (-3) = 0 

CORRECTING DEFECT 20 (vertices=26, convex hull=68, v0=140266)
After retessellation of defect 20 (v0=140266), euler #=-2 (151443,454223,302778) : difference with theory (-2) = 0 

CORRECTING DEFECT 21 (vertices=33, convex hull=73, v0=143316)
After retessellation of defect 21 (v0=143316), euler #=-1 (151460,454306,302845) : difference with theory (-1) = 0 

CORRECTING DEFECT 22 (vertices=28, convex hull=66, v0=147408)
After retessellation of defect 22 (v0=147408), euler #=0 (151468,454354,302886) : difference with theory (0) = 0 

CORRECTING DEFECT 23 (vertices=40, convex hull=56, v0=150693)
After retessellation of defect 23 (v0=150693), euler #=1 (151485,454428,302944) : difference with theory (1) = 0 

CORRECTING DEFECT 24 (vertices=21, convex hull=64, v0=151494)
After retessellation of defect 24 (v0=151494), euler #=2 (151498,454488,302992) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.21 (0.05-->8.60) (max @ vno 124246 --> 131151)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.21 (0.05-->8.60) (max @ vno 124246 --> 131151)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
117 mutations (35.9%), 209 crossovers (64.1%), 78 vertices were eliminated
building final representation...
1094 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=151498, nf=302992, ne=454488, g=0)
writing corrected surface to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 11.0 minutes
0 defective edges
removing intersecting faces
000: 150 intersecting
001: 18 intersecting
mris_fix_topology utimesec    659.536000
mris_fix_topology stimesec    0.268000
mris_fix_topology ru_maxrss   479652
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   118896
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  0
mris_fix_topology ru_oublock  14256
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    114
mris_fix_topology ru_nivcsw   1628
FSRUNTIME@ mris_fix_topology rh  0.1833 hours 1 threads

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 148761 - 446277 + 297518 = 2 --> 0 holes
      F =2V-4:          297518 = 297522-4 (0)
      2E=3F:            892554 = 892554 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 151498 - 454488 + 302992 = 2 --> 0 holes
      F =2V-4:          302992 = 302996-4 (0)
      2E=3F:            908976 = 908976 (0)

total defect index = 0
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_remove_intersection ../surf/lh.orig ../surf/lh.orig 

intersection removal took 0.00 hours
removing intersecting faces
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_remove_intersection ../surf/rh.orig ../surf/rh.orig 

intersection removal took 0.00 hours
removing intersecting faces
000: 15 intersecting
001: 6 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Mon Feb 15 20:38:03 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs stripped lh 

using white.preaparc as white matter name...
only generating white matter surface
using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline
not using aparc to prevent surfaces crossing the midline
INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $
$Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/filled.mgz...
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/brain.finalsurfs.mgz...
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/../mri/aseg.presurf.mgz...
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/wm.mgz...
26904 bright wm thresholded.
515 bright non-wm voxels segmented.
reading original surface position from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.orig...
computing class statistics...
border white:    280914 voxels (1.67%)
border gray      308996 voxels (1.84%)
WM (102.0): 101.5 +- 6.8 [70.0 --> 110.0]
GM (80.0) : 79.2 +- 10.2 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 66.8 (was 70)
setting MAX_BORDER_WHITE to 112.8 (was 105)
setting MIN_BORDER_WHITE to 77.0 (was 85)
setting MAX_CSF to 56.5 (was 40)
setting MAX_GRAY to 99.2 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 66.8 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 46.3 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.21 (0.01-->4.13) (max @ vno 64037 --> 148510)
face area 0.28 +- 0.12 (0.00-->2.51)
mean absolute distance = 0.78 +- 0.98
4329 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106+-4.3,    GM=77+-7.0
mean inside = 98.0, mean outside = 82.7
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=86.0, 32 (32) missing vertices, mean dist 0.3 [0.7 (%34.0)->0.8 (%66.0))]
%60 local maxima, %36 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=mercu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.25 (0.07-->4.66) (max @ vno 77416 --> 72693)
face area 0.28 +- 0.13 (0.00-->2.29)
mean absolute distance = 0.41 +- 0.65
3658 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2853674.5, rms=8.860
001: dt: 0.5000, sse=1703505.1, rms=6.250 (29.459%)
002: dt: 0.5000, sse=1168194.2, rms=4.517 (27.727%)
003: dt: 0.5000, sse=917975.4, rms=3.414 (24.419%)
004: dt: 0.5000, sse=805328.1, rms=2.771 (18.841%)
005: dt: 0.5000, sse=763360.9, rms=2.475 (10.657%)
006: dt: 0.5000, sse=742665.6, rms=2.331 (5.828%)
rms = 2.28, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=738570.1, rms=2.284 (2.025%)
008: dt: 0.2500, sse=661186.6, rms=1.436 (37.113%)
009: dt: 0.2500, sse=649872.6, rms=1.288 (10.297%)
rms = 1.25, time step reduction 2 of 3 to 0.125...
010: dt: 0.2500, sse=647263.3, rms=1.254 (2.675%)
rms = 1.23, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=645663.2, rms=1.233 (1.698%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=88.9, 30 (8) missing vertices, mean dist -0.3 [0.5 (%72.6)->0.2 (%27.4))]
%72 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=mercu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.24 (0.08-->5.29) (max @ vno 77416 --> 72693)
face area 0.35 +- 0.16 (0.00-->3.23)
mean absolute distance = 0.29 +- 0.41
4545 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1286927.1, rms=4.329
012: dt: 0.5000, sse=963149.2, rms=2.734 (36.855%)
013: dt: 0.5000, sse=886200.4, rms=2.180 (20.242%)
014: dt: 0.5000, sse=851076.8, rms=1.915 (12.190%)
rms = 1.94, time step reduction 1 of 3 to 0.250...
015: dt: 0.2500, sse=812718.9, rms=1.480 (22.719%)
016: dt: 0.2500, sse=793332.6, rms=1.195 (19.225%)
017: dt: 0.2500, sse=787530.7, rms=1.107 (7.398%)
rms = 1.08, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=785634.8, rms=1.076 (2.739%)
rms = 1.06, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=784361.6, rms=1.060 (1.553%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=91.6, 22 (6) missing vertices, mean dist -0.2 [0.3 (%77.1)->0.2 (%22.9))]
%85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=mercu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.24 (0.05-->5.67) (max @ vno 77416 --> 72693)
face area 0.34 +- 0.15 (0.00-->3.33)
mean absolute distance = 0.21 +- 0.31
3891 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1034638.8, rms=3.332
020: dt: 0.5000, sse=823168.9, rms=1.851 (44.463%)
021: dt: 0.5000, sse=809507.4, rms=1.764 (4.660%)
rms = 1.72, time step reduction 1 of 3 to 0.250...
022: dt: 0.5000, sse=803970.3, rms=1.724 (2.288%)
023: dt: 0.2500, sse=754170.4, rms=1.061 (38.471%)
024: dt: 0.2500, sse=751167.8, rms=0.966 (8.895%)
rms = 0.97, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=748250.6, rms=0.966 (0.022%)
rms = 0.95, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=747198.4, rms=0.950 (1.657%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
mean border=92.4, 20 (4) missing vertices, mean dist -0.1 [0.2 (%60.5)->0.2 (%39.5))]
%89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=mercu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=763192.9, rms=1.444
027: dt: 0.5000, sse=740173.2, rms=1.090 (24.534%)
rms = 1.39, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=724824.0, rms=0.831 (23.702%)
029: dt: 0.2500, sse=723858.6, rms=0.773 (7.008%)
rms = 0.75, time step reduction 2 of 3 to 0.125...
030: dt: 0.2500, sse=720394.8, rms=0.746 (3.547%)
rms = 0.75, time step reduction 3 of 3 to 0.062...
031: dt: 0.1250, sse=719286.5, rms=0.747 (-0.176%)
positioning took 0.5 minutes
generating cortex label...
11 non-cortical segments detected
only using segment with 7830 vertices
erasing segment 1 (vno[0] = 107598)
erasing segment 2 (vno[0] = 107766)
erasing segment 3 (vno[0] = 108658)
erasing segment 4 (vno[0] = 108689)
erasing segment 5 (vno[0] = 109508)
erasing segment 6 (vno[0] = 109569)
erasing segment 7 (vno[0] = 111718)
erasing segment 8 (vno[0] = 112671)
erasing segment 9 (vno[0] = 116519)
erasing segment 10 (vno[0] = 116533)
writing cortex label to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/lh.cortex.label...
writing curvature file /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.area
vertex spacing 0.88 +- 0.24 (0.01-->5.85) (max @ vno 72693 --> 77416)
face area 0.33 +- 0.15 (0.00-->3.29)
refinement took 4.2 minutes
#--------------------------------------------
#@# Make White Surf rh Mon Feb 15 20:42:14 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs stripped rh 

using white.preaparc as white matter name...
only generating white matter surface
using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline
not using aparc to prevent surfaces crossing the midline
INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $
$Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/filled.mgz...
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/brain.finalsurfs.mgz...
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/../mri/aseg.presurf.mgz...
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/wm.mgz...
26904 bright wm thresholded.
515 bright non-wm voxels segmented.
reading original surface position from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.orig...
computing class statistics...
border white:    280914 voxels (1.67%)
border gray      308996 voxels (1.84%)
WM (102.0): 101.5 +- 6.8 [70.0 --> 110.0]
GM (80.0) : 79.2 +- 10.2 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 67.8 (was 70)
setting MAX_BORDER_WHITE to 112.8 (was 105)
setting MIN_BORDER_WHITE to 78.0 (was 85)
setting MAX_CSF to 57.5 (was 40)
setting MAX_GRAY to 99.2 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 67.8 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 47.3 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.21 (0.02-->3.36) (max @ vno 131151 --> 131899)
face area 0.28 +- 0.12 (0.00-->2.31)
mean absolute distance = 0.76 +- 0.97
3750 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106+-4.3,    GM=78+-6.1
mean inside = 98.0, mean outside = 82.6
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=86.6, 50 (50) missing vertices, mean dist 0.3 [0.7 (%36.6)->0.8 (%63.4))]
%58 local maxima, %38 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=mercu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.24 (0.13-->3.41) (max @ vno 107193 --> 107213)
face area 0.28 +- 0.13 (0.00-->2.18)
mean absolute distance = 0.38 +- 0.63
3663 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2847019.0, rms=8.753
001: dt: 0.5000, sse=1688000.9, rms=6.110 (30.191%)
002: dt: 0.5000, sse=1161763.5, rms=4.404 (27.930%)
003: dt: 0.5000, sse=926890.4, rms=3.370 (23.469%)
004: dt: 0.5000, sse=823217.5, rms=2.787 (17.295%)
005: dt: 0.5000, sse=785109.8, rms=2.538 (8.956%)
006: dt: 0.5000, sse=770369.1, rms=2.429 (4.262%)
rms = 2.40, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=767129.8, rms=2.402 (1.138%)
008: dt: 0.2500, sse=684204.4, rms=1.576 (34.362%)
009: dt: 0.2500, sse=672889.8, rms=1.439 (8.689%)
rms = 1.41, time step reduction 2 of 3 to 0.125...
010: dt: 0.2500, sse=670638.6, rms=1.408 (2.158%)
rms = 1.38, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=669341.8, rms=1.385 (1.678%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
mean border=89.3, 15 (4) missing vertices, mean dist -0.3 [0.4 (%71.7)->0.2 (%28.3))]
%70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=mercu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.23 (0.07-->3.37) (max @ vno 131151 --> 131897)
face area 0.35 +- 0.15 (0.00-->2.83)
mean absolute distance = 0.29 +- 0.40
4710 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1260121.1, rms=4.130
012: dt: 0.5000, sse=946615.9, rms=2.518 (39.017%)
013: dt: 0.5000, sse=880652.9, rms=2.042 (18.917%)
014: dt: 0.5000, sse=855996.7, rms=1.849 (9.468%)
rms = 1.95, time step reduction 1 of 3 to 0.250...
015: dt: 0.2500, sse=817469.0, rms=1.388 (24.925%)
016: dt: 0.2500, sse=800461.6, rms=1.133 (18.396%)
017: dt: 0.2500, sse=797064.4, rms=1.075 (5.115%)
rms = 1.06, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=796722.3, rms=1.061 (1.263%)
rms = 1.05, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=795719.1, rms=1.047 (1.340%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=91.8, 9 (1) missing vertices, mean dist -0.2 [0.3 (%75.8)->0.2 (%24.2))]
%84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=mercu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.23 (0.09-->3.48) (max @ vno 151272 --> 81042)
face area 0.34 +- 0.15 (0.00-->2.86)
mean absolute distance = 0.21 +- 0.30
3861 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1028948.1, rms=3.188
020: dt: 0.5000, sse=842613.0, rms=1.892 (40.655%)
021: dt: 0.5000, sse=829193.2, rms=1.782 (5.820%)
rms = 1.74, time step reduction 1 of 3 to 0.250...
022: dt: 0.5000, sse=821052.4, rms=1.735 (2.617%)
023: dt: 0.2500, sse=770116.4, rms=1.071 (38.297%)
024: dt: 0.2500, sse=763789.8, rms=0.974 (9.056%)
rms = 0.97, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=763648.5, rms=0.973 (0.096%)
rms = 0.96, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=762307.7, rms=0.956 (1.739%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=92.7, 30 (1) missing vertices, mean dist -0.1 [0.2 (%59.7)->0.2 (%40.3))]
%88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=mercu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=775487.6, rms=1.414
027: dt: 0.5000, sse=754346.1, rms=1.077 (23.840%)
rms = 1.38, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=739183.7, rms=0.832 (22.776%)
029: dt: 0.2500, sse=735755.0, rms=0.775 (6.843%)
rms = 0.75, time step reduction 2 of 3 to 0.125...
030: dt: 0.2500, sse=733653.8, rms=0.750 (3.250%)
rms = 0.75, time step reduction 3 of 3 to 0.062...
031: dt: 0.1250, sse=733023.0, rms=0.749 (0.067%)
positioning took 0.5 minutes
generating cortex label...
8 non-cortical segments detected
only using segment with 7655 vertices
erasing segment 1 (vno[0] = 107158)
erasing segment 2 (vno[0] = 107165)
erasing segment 3 (vno[0] = 108238)
erasing segment 4 (vno[0] = 110360)
erasing segment 5 (vno[0] = 111474)
erasing segment 6 (vno[0] = 111492)
erasing segment 7 (vno[0] = 117283)
writing cortex label to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/rh.cortex.label...
writing curvature file /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.area
vertex spacing 0.88 +- 0.24 (0.04-->3.45) (max @ vno 81042 --> 151272)
face area 0.33 +- 0.15 (0.00-->2.80)
refinement took 4.2 minutes
#--------------------------------------------
#@# Smooth2 lh Mon Feb 15 20:46:28 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm 

smoothing for 3 iterations
setting seed for random number generator to 1234
smoothing surface tessellation for 3 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Smooth2 rh Mon Feb 15 20:46:33 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm 

smoothing for 3 iterations
setting seed for random number generator to 1234
smoothing surface tessellation for 3 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Inflation2 lh Mon Feb 15 20:46:38 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_inflate -rusage /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

Reading ../surf/lh.smoothwm
avg radius = 48.6 mm, total surface area = 88812 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc
step 000: RMS=0.173 (target=0.015)   step 005: RMS=0.121 (target=0.015)   step 010: RMS=0.088 (target=0.015)   step 015: RMS=0.072 (target=0.015)   step 020: RMS=0.060 (target=0.015)   step 025: RMS=0.050 (target=0.015)   step 030: RMS=0.042 (target=0.015)   step 035: RMS=0.036 (target=0.015)   step 040: RMS=0.032 (target=0.015)   step 045: RMS=0.029 (target=0.015)   step 050: RMS=0.026 (target=0.015)   step 055: RMS=0.025 (target=0.015)   step 060: RMS=0.023 (target=0.015)   
inflation complete.
inflation took 0.5 minutes
mris_inflate utimesec    28.352000
mris_inflate stimesec    0.084000
mris_inflate ru_maxrss   195916
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   47353
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11640
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    62
mris_inflate ru_nivcsw   367
#--------------------------------------------
#@# Inflation2 rh Mon Feb 15 20:47:06 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_inflate -rusage /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Reading ../surf/rh.smoothwm
avg radius = 49.2 mm, total surface area = 90464 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc
step 000: RMS=0.173 (target=0.015)   step 005: RMS=0.120 (target=0.015)   step 010: RMS=0.087 (target=0.015)   step 015: RMS=0.071 (target=0.015)   step 020: RMS=0.058 (target=0.015)   step 025: RMS=0.049 (target=0.015)   step 030: RMS=0.041 (target=0.015)   step 035: RMS=0.034 (target=0.015)   step 040: RMS=0.030 (target=0.015)   step 045: RMS=0.026 (target=0.015)   step 050: RMS=0.024 (target=0.015)   step 055: RMS=0.022 (target=0.015)   step 060: RMS=0.021 (target=0.015)   
inflation complete.
inflation took 0.5 minutes
mris_inflate utimesec    28.472000
mris_inflate stimesec    0.100000
mris_inflate ru_maxrss   199348
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   48234
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11848
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    72
mris_inflate ru_nivcsw   514
#--------------------------------------------
#@# Curv .H and .K lh Mon Feb 15 20:47:35 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf

 mris_curvature -w lh.white.preaparc 

total integrated curvature = 0.952*4pi (11.962) --> 0 handles
ICI = 158.9, FI = 1805.5, variation=27954.111
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
rm -f lh.white.K
ln -s lh.white.preaparc.K lh.white.K

 mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated 

normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
185 vertices thresholded to be in k1 ~ [-0.30 0.38], k2 ~ [-0.14 0.10]
total integrated curvature = 0.565*4pi (7.104) --> 0 handles
ICI = 1.5, FI = 9.8, variation=166.424
141 vertices thresholded to be in [-0.03 0.01]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
136 vertices thresholded to be in [-0.12 0.15]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.022
done.
#--------------------------------------------
#@# Curv .H and .K rh Mon Feb 15 20:48:41 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf

 mris_curvature -w rh.white.preaparc 

total integrated curvature = -0.062*4pi (-0.774) --> 1 handles
ICI = 158.1, FI = 1820.8, variation=28142.853
writing Gaussian curvature to ./rh.white.preaparc.K...done.
writing mean curvature to ./rh.white.preaparc.H...done.
rm -f rh.white.H
ln -s rh.white.preaparc.H rh.white.H
rm -f rh.white.K
ln -s rh.white.preaparc.K rh.white.K

 mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated 

normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
183 vertices thresholded to be in k1 ~ [-0.27 0.35], k2 ~ [-0.16 0.07]
total integrated curvature = 0.588*4pi (7.390) --> 0 handles
ICI = 1.5, FI = 10.8, variation=178.121
150 vertices thresholded to be in [-0.02 0.01]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
139 vertices thresholded to be in [-0.14 0.16]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.023
done.

#-----------------------------------------
#@# Curvature Stats lh Mon Feb 15 20:49:48 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm stripped lh curv sulc 

             Toggling save flag on curvature files                       [ ok ]
                 Outputting results using filestem   [ ../stats/lh.curv.stats ]
             Toggling save flag on curvature files                       [ ok ]
                                   Setting surface     [ stripped/lh.smoothwm ]
                                Reading surface...                       [ ok ]
                                   Setting texture                     [ curv ]
                                Reading texture...                       [ ok ]
                                   Setting texture                     [ sulc ]
                                Reading texture...Gb_filter = 0
                       [ ok ]
      Calculating Discrete Principal Curvatures...
   Determining geometric order for vertex faces... [####################] [ ok ]
                      Determining KH curvatures... [####################] [ ok ]
                    Determining k1k2 curvatures... [####################] [ ok ]
                                   deltaViolations                      [ 285 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.231339
WARN:    S explicit min:                          0.000000	vertex = 779

#-----------------------------------------
#@# Curvature Stats rh Mon Feb 15 20:49:52 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm stripped rh curv sulc 

             Toggling save flag on curvature files                       [ ok ]
                 Outputting results using filestem   [ ../stats/rh.curv.stats ]
             Toggling save flag on curvature files                       [ ok ]
                                   Setting surface     [ stripped/rh.smoothwm ]
                                Reading surface...                       [ ok ]
                                   Setting texture                     [ curv ]
                                Reading texture...                       [ ok ]
                                   Setting texture                     [ sulc ]
                                Reading texture...Gb_filter = 0
                       [ ok ]
      Calculating Discrete Principal Curvatures...
   Determining geometric order for vertex faces... [####################] [ ok ]
                      Determining KH curvatures... [####################] [ ok ]
                    Determining k1k2 curvatures... [####################] [ ok ]
                                   deltaViolations                      [ 250 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.471104
WARN:    S explicit min:                          0.000000	vertex = 429
#--------------------------------------------
#@# Sphere lh Mon Feb 15 20:49:55 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_sphere -rusage /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...

== Number of threads available to mris_sphere for OpenMP = 1 == 
scaling brain by 0.284...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=mercu, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %19.62
pass 1: epoch 2 of 3 starting distance error %19.56
unfolding complete - removing small folds...
starting distance error %19.48
removing remaining folds...
final distance error %19.49
MRISunfold() return, current seed 1234
-01: dt=0.0000, 205 negative triangles
161: dt=0.9900, 205 negative triangles
162: dt=0.9900, 112 negative triangles
163: dt=0.9900, 99 negative triangles
164: dt=0.9900, 90 negative triangles
165: dt=0.9900, 87 negative triangles
166: dt=0.9900, 73 negative triangles
167: dt=0.9900, 75 negative triangles
168: dt=0.9900, 77 negative triangles
169: dt=0.9900, 72 negative triangles
170: dt=0.9900, 72 negative triangles
171: dt=0.9900, 58 negative triangles
172: dt=0.9900, 66 negative triangles
173: dt=0.9900, 63 negative triangles
174: dt=0.9900, 69 negative triangles
175: dt=0.9900, 64 negative triangles
176: dt=0.9900, 67 negative triangles
177: dt=0.9900, 68 negative triangles
178: dt=0.9900, 63 negative triangles
179: dt=0.9900, 56 negative triangles
180: dt=0.9900, 65 negative triangles
181: dt=0.9900, 55 negative triangles
182: dt=0.9900, 57 negative triangles
183: dt=0.9900, 51 negative triangles
184: dt=0.9900, 52 negative triangles
185: dt=0.9900, 55 negative triangles
186: dt=0.9900, 49 negative triangles
187: dt=0.9900, 58 negative triangles
188: dt=0.9900, 53 negative triangles
189: dt=0.9900, 55 negative triangles
190: dt=0.9900, 51 negative triangles
191: dt=0.9900, 54 negative triangles
192: dt=0.9900, 50 negative triangles
193: dt=0.9900, 51 negative triangles
194: dt=0.9900, 45 negative triangles
195: dt=0.9900, 49 negative triangles
196: dt=0.9900, 47 negative triangles
197: dt=0.9900, 43 negative triangles
198: dt=0.9900, 45 negative triangles
199: dt=0.9900, 38 negative triangles
200: dt=0.9900, 46 negative triangles
201: dt=0.9900, 38 negative triangles
202: dt=0.9900, 39 negative triangles
203: dt=0.9900, 43 negative triangles
204: dt=0.9900, 37 negative triangles
205: dt=0.9900, 41 negative triangles
206: dt=0.9900, 41 negative triangles
207: dt=0.9900, 38 negative triangles
208: dt=0.9900, 46 negative triangles
209: dt=0.9900, 39 negative triangles
210: dt=0.9900, 37 negative triangles
211: dt=0.9900, 40 negative triangles
212: dt=0.9900, 37 negative triangles
213: dt=0.9900, 37 negative triangles
214: dt=0.9405, 38 negative triangles
215: dt=0.9405, 37 negative triangles
216: dt=0.9405, 31 negative triangles
217: dt=0.9405, 31 negative triangles
218: dt=0.9405, 31 negative triangles
219: dt=0.9405, 32 negative triangles
220: dt=0.9405, 31 negative triangles
221: dt=0.9405, 35 negative triangles
222: dt=0.9405, 29 negative triangles
223: dt=0.9405, 32 negative triangles
224: dt=0.9405, 28 negative triangles
225: dt=0.9405, 30 negative triangles
226: dt=0.9405, 29 negative triangles
227: dt=0.9405, 28 negative triangles
228: dt=0.9405, 28 negative triangles
229: dt=0.9405, 27 negative triangles
230: dt=0.9405, 20 negative triangles
231: dt=0.9405, 19 negative triangles
232: dt=0.9405, 23 negative triangles
233: dt=0.9405, 17 negative triangles
234: dt=0.9405, 20 negative triangles
235: dt=0.9405, 16 negative triangles
236: dt=0.9405, 15 negative triangles
237: dt=0.9405, 13 negative triangles
238: dt=0.9405, 16 negative triangles
239: dt=0.9405, 13 negative triangles
240: dt=0.9405, 9 negative triangles
241: dt=0.9405, 13 negative triangles
242: dt=0.9405, 10 negative triangles
243: dt=0.9405, 7 negative triangles
244: dt=0.9405, 6 negative triangles
245: dt=0.9405, 7 negative triangles
246: dt=0.9405, 7 negative triangles
247: dt=0.9405, 5 negative triangles
248: dt=0.9405, 3 negative triangles
249: dt=0.9405, 2 negative triangles
250: dt=0.9405, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 0.56 hours
mris_sphere utimesec    2032.480000
mris_sphere stimesec    0.364000
mris_sphere ru_maxrss   267884
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   65268
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10472
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    100
mris_sphere ru_nivcsw   9741
FSRUNTIME@ mris_sphere  0.5647 hours 1 threads
#--------------------------------------------
#@# Sphere rh Mon Feb 15 21:23:48 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_sphere -rusage /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...

== Number of threads available to mris_sphere for OpenMP = 1 == 
scaling brain by 0.278...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=mercu, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.05
pass 1: epoch 2 of 3 starting distance error %20.02
unfolding complete - removing small folds...
starting distance error %19.90
removing remaining folds...
final distance error %19.91
MRISunfold() return, current seed 1234
-01: dt=0.0000, 67 negative triangles
201: dt=0.9900, 67 negative triangles
202: dt=0.9900, 21 negative triangles
203: dt=0.9900, 13 negative triangles
204: dt=0.9900, 16 negative triangles
205: dt=0.9900, 10 negative triangles
206: dt=0.9900, 5 negative triangles
207: dt=0.9900, 5 negative triangles
208: dt=0.9900, 4 negative triangles
209: dt=0.9900, 3 negative triangles
210: dt=0.9900, 1 negative triangles
211: dt=0.9900, 3 negative triangles
212: dt=0.9900, 1 negative triangles
213: dt=0.9900, 1 negative triangles
214: dt=0.9900, 3 negative triangles
215: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 0.65 hours
mris_sphere utimesec    2352.916000
mris_sphere stimesec    0.312000
mris_sphere ru_maxrss   272564
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   66421
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10664
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    69
mris_sphere ru_nivcsw   3656
FSRUNTIME@ mris_sphere  0.6537 hours 1 threads
#--------------------------------------------
#@# Surf Reg lh Mon Feb 15 22:03:02 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_register -curv -rusage /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /airflow/apps/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 

using smoothwm curvature for final alignment

cwd /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts
cmdline mris_register -curv -rusage /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /airflow/apps/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 

0 inflated.H
1 sulc
2 smoothwm (computed)
$Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading surface from ../surf/lh.sphere...
reading template parameterization from /airflow/apps/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif...
MRISregister() -------
max_passes = 4 
min_degrees = 0.500000 
max_degrees = 64.000000 
nangles = 8 
tol=5.0e-01, sigma=0.0, host=mercu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height -1.000000
momentum 0.950000
nbhd_size -10
max_nbrs 10
niterations 25
nsurfaces 0
SURFACES 3
flags 16 (10)
use curv 16
no sulc 0
no rigid align 0
mris->nsize 1
mris->hemisphere 0
randomSeed 0

tol=5.0e-01, sigma=0.0, host=mercu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
--------------------
1 Reading lh.sulc
curvature mean = -0.000, std = 5.477
curvature mean = 0.022, std = 0.819
curvature mean = 0.024, std = 0.853
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 0.00) sse = 345305.2, tmin=0.7618
  d=32.00 min @ (-8.00, 0.00, 0.00) sse = 273679.8, tmin=1.5315
  d=16.00 min @ (0.00, -4.00, 4.00) sse = 243313.8, tmin=2.3005
  d=8.00 min @ (0.00, 0.00, -2.00) sse = 237215.4, tmin=3.0836
  d=4.00 min @ (-1.00, 0.00, 1.00) sse = 234401.8, tmin=3.8704
  d=2.00 min @ (0.00, 0.50, -0.50) sse = 233793.0, tmin=4.6595
  d=1.00 min @ (0.00, -0.25, 0.00) sse = 233719.8, tmin=5.4435
tol=1.0e+00, sigma=0.5, host=mercu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   6.22 min
curvature mean = -0.005, std = 0.833
curvature mean = 0.011, std = 0.940
curvature mean = -0.007, std = 0.843
curvature mean = 0.005, std = 0.974
curvature mean = -0.009, std = 0.844
curvature mean = 0.001, std = 0.989
2 Reading smoothwm
curvature mean = -0.027, std = 0.285
curvature mean = 0.037, std = 0.247
curvature mean = 0.069, std = 0.347
curvature mean = 0.035, std = 0.304
curvature mean = 0.034, std = 0.543
curvature mean = 0.034, std = 0.330
curvature mean = 0.018, std = 0.690
curvature mean = 0.035, std = 0.341
curvature mean = 0.007, std = 0.801
MRISregister() return, current seed 0
-01: dt=0.0000, 61 negative triangles
120: dt=0.9900, 61 negative triangles
expanding nbhd size to 1
121: dt=0.9900, 85 negative triangles
122: dt=0.9900, 65 negative triangles
123: dt=0.9900, 63 negative triangles
124: dt=0.9900, 61 negative triangles
125: dt=0.9900, 61 negative triangles
126: dt=0.9900, 53 negative triangles
127: dt=0.9900, 52 negative triangles
128: dt=0.9900, 49 negative triangles
129: dt=0.9900, 48 negative triangles
130: dt=0.9900, 35 negative triangles
131: dt=0.9900, 37 negative triangles
132: dt=0.9900, 35 negative triangles
133: dt=0.9900, 27 negative triangles
134: dt=0.9900, 28 negative triangles
135: dt=0.9900, 20 negative triangles
136: dt=0.9900, 23 negative triangles
137: dt=0.9900, 20 negative triangles
138: dt=0.9900, 19 negative triangles
139: dt=0.9900, 16 negative triangles
140: dt=0.9900, 14 negative triangles
141: dt=0.9900, 11 negative triangles
142: dt=0.9900, 9 negative triangles
143: dt=0.9900, 7 negative triangles
144: dt=0.9900, 7 negative triangles
145: dt=0.9900, 4 negative triangles
146: dt=0.9900, 5 negative triangles
147: dt=0.9900, 2 negative triangles
148: dt=0.9900, 2 negative triangles
149: dt=0.9900, 3 negative triangles
150: dt=0.9900, 1 negative triangles
151: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 0.79 hours
mris_register utimesec    2828.940000
mris_register stimesec    0.684000
mris_register ru_maxrss   248368
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   60299
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10472
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    86
mris_register ru_nivcsw   3698
FSRUNTIME@ mris_register  0.7860 hours 1 threads
#--------------------------------------------
#@# Surf Reg rh Mon Feb 15 22:50:11 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_register -curv -rusage /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /airflow/apps/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 

using smoothwm curvature for final alignment

cwd /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts
cmdline mris_register -curv -rusage /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /airflow/apps/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 

0 inflated.H
1 sulc
2 smoothwm (computed)
$Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading surface from ../surf/rh.sphere...
reading template parameterization from /airflow/apps/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif...
MRISregister() -------
max_passes = 4 
min_degrees = 0.500000 
max_degrees = 64.000000 
nangles = 8 
tol=5.0e-01, sigma=0.0, host=mercu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height -1.000000
momentum 0.950000
nbhd_size -10
max_nbrs 10
niterations 25
nsurfaces 0
SURFACES 3
flags 16 (10)
use curv 16
no sulc 0
no rigid align 0
mris->nsize 1
mris->hemisphere 1
randomSeed 0

tol=5.0e-01, sigma=0.0, host=mercu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
--------------------
1 Reading rh.sulc
curvature mean = 0.000, std = 5.514
curvature mean = 0.023, std = 0.813
curvature mean = 0.024, std = 0.852
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 0.00) sse = 360652.4, tmin=0.7665
  d=32.00 min @ (-8.00, 0.00, 8.00) sse = 273361.7, tmin=1.5464
  d=16.00 min @ (0.00, -4.00, -4.00) sse = 259084.3, tmin=2.3333
  d=8.00 min @ (2.00, 2.00, 2.00) sse = 242436.0, tmin=3.1315
  d=4.00 min @ (-1.00, 0.00, -1.00) sse = 242251.3, tmin=3.9362
  d=2.00 min @ (0.50, 0.00, 0.50) sse = 241341.3, tmin=4.7427
  d=1.00 min @ (0.00, 0.25, 0.00) sse = 241335.0, tmin=5.5461
  d=0.50 min @ (0.00, -0.12, 0.00) sse = 241306.0, tmin=6.3494
tol=1.0e+00, sigma=0.5, host=mercu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   6.35 min
curvature mean = -0.010, std = 0.820
curvature mean = 0.008, std = 0.944
curvature mean = -0.017, std = 0.827
curvature mean = 0.003, std = 0.978
curvature mean = -0.020, std = 0.827
curvature mean = 0.001, std = 0.992
2 Reading smoothwm
curvature mean = -0.026, std = 0.271
curvature mean = 0.030, std = 0.240
curvature mean = 0.068, std = 0.361
curvature mean = 0.027, std = 0.297
curvature mean = 0.032, std = 0.569
curvature mean = 0.027, std = 0.323
curvature mean = 0.016, std = 0.721
curvature mean = 0.027, std = 0.334
curvature mean = 0.005, std = 0.829
MRISregister() return, current seed 0
-01: dt=0.0000, 24 negative triangles
120: dt=0.9900, 24 negative triangles
expanding nbhd size to 1
121: dt=0.9900, 24 negative triangles
122: dt=0.9900, 20 negative triangles
123: dt=0.9900, 20 negative triangles
124: dt=0.9900, 20 negative triangles
125: dt=0.9900, 17 negative triangles
126: dt=0.9900, 18 negative triangles
127: dt=0.9900, 17 negative triangles
128: dt=0.9900, 15 negative triangles
129: dt=0.9900, 14 negative triangles
130: dt=0.9900, 14 negative triangles
131: dt=0.9900, 11 negative triangles
132: dt=0.9900, 11 negative triangles
133: dt=0.9900, 10 negative triangles
134: dt=0.9900, 11 negative triangles
135: dt=0.9900, 7 negative triangles
136: dt=0.9900, 7 negative triangles
137: dt=0.9900, 5 negative triangles
138: dt=0.9900, 6 negative triangles
139: dt=0.9900, 5 negative triangles
140: dt=0.9900, 6 negative triangles
141: dt=0.9900, 6 negative triangles
142: dt=0.9900, 7 negative triangles
143: dt=0.9900, 4 negative triangles
144: dt=0.9900, 1 negative triangles
145: dt=0.9900, 1 negative triangles
146: dt=0.9900, 1 negative triangles
147: dt=0.9900, 2 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 0.80 hours
mris_register utimesec    2867.580000
mris_register stimesec    0.628000
mris_register ru_maxrss   251824
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   61180
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10664
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    72
mris_register ru_nivcsw   8707
FSRUNTIME@ mris_register  0.7968 hours 1 threads
#--------------------------------------------
#@# Jacobian white lh Mon Feb 15 23:38:00 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white 

reading surface from ../surf/lh.white.preaparc...
writing curvature file ../surf/lh.jacobian_white
#--------------------------------------------
#@# Jacobian white rh Mon Feb 15 23:38:02 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white 

reading surface from ../surf/rh.white.preaparc...
writing curvature file ../surf/rh.jacobian_white
#--------------------------------------------
#@# AvgCurv lh Mon Feb 15 23:38:03 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mrisp_paint -a 5 /airflow/apps/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv 

averaging curvature patterns 5 times...
reading surface from ../surf/lh.sphere.reg...
reading template parameterization from /airflow/apps/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif...
writing curvature file to ../surf/lh.avg_curv...
#--------------------------------------------
#@# AvgCurv rh Mon Feb 15 23:38:05 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mrisp_paint -a 5 /airflow/apps/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv 

averaging curvature patterns 5 times...
reading surface from ../surf/rh.sphere.reg...
reading template parameterization from /airflow/apps/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif...
writing curvature file to ../surf/rh.avg_curv...
#-----------------------------------------
#@# Cortical Parc lh Mon Feb 15 23:38:06 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 stripped lh ../surf/lh.sphere.reg /airflow/apps/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot 

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /airflow/apps/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 0.8   using min determinant for regularization = 0.006
0 singular and 342 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1297 labels changed using aseg
relabeling using gibbs priors...
000:   3438 changed, 148761 examined...
001:    807 changed, 14383 examined...
002:    182 changed, 4383 examined...
003:     56 changed, 1088 examined...
004:     24 changed, 324 examined...
005:     11 changed, 156 examined...
006:     11 changed, 65 examined...
007:      2 changed, 57 examined...
008:      2 changed, 12 examined...
009:      0 changed, 15 examined...
258 labels changed using aseg
000: 129 total segments, 89 labels (296 vertices) changed
001: 42 total segments, 4 labels (13 vertices) changed
002: 38 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 23 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2085 vertices marked for relabeling...
2085 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 11 seconds.
#-----------------------------------------
#@# Cortical Parc rh Mon Feb 15 23:38:18 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 stripped rh ../surf/rh.sphere.reg /airflow/apps/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot 

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /airflow/apps/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 0.7   using min determinant for regularization = 0.004
0 singular and 309 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
865 labels changed using aseg
relabeling using gibbs priors...
000:   3026 changed, 151498 examined...
001:    698 changed, 13026 examined...
002:    175 changed, 3983 examined...
003:     68 changed, 1088 examined...
004:     13 changed, 439 examined...
005:      4 changed, 90 examined...
006:      0 changed, 26 examined...
169 labels changed using aseg
000: 99 total segments, 50 labels (298 vertices) changed
001: 49 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 5 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1627 vertices marked for relabeling...
1627 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 11 seconds.
#--------------------------------------------
#@# Make Pial Surf lh Mon Feb 15 23:38:29 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs stripped lh 

using white.preaparc starting white location...
using white.preaparc starting pial locations...
using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline
INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $
$Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/filled.mgz...
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/brain.finalsurfs.mgz...
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/../mri/aseg.presurf.mgz...
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/wm.mgz...
26904 bright wm thresholded.
515 bright non-wm voxels segmented.
reading original surface position from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.orig...
computing class statistics...
border white:    280914 voxels (1.67%)
border gray      308996 voxels (1.84%)
WM (102.0): 101.5 +- 6.8 [70.0 --> 110.0]
GM (80.0) : 79.2 +- 10.2 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 66.8 (was 70)
setting MAX_BORDER_WHITE to 112.8 (was 105)
setting MIN_BORDER_WHITE to 77.0 (was 85)
setting MAX_CSF to 56.5 (was 40)
setting MAX_GRAY to 99.2 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 66.8 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 46.3 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106+-4.3,    GM=77+-7.0
mean inside = 98.0, mean outside = 82.7
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.88 +- 0.24 (0.01-->5.85) (max @ vno 72693 --> 77416)
face area 0.33 +- 0.15 (0.00-->3.25)
mean absolute distance = 0.76 +- 0.93
2782 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 36 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 47 points - only 0.00% unknown
deleting segment 5 with 53 points - only 0.00% unknown
deleting segment 6 with 101 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 9 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 10 with 1 points - only 0.00% unknown
mean border=86.0, 38 (36) missing vertices, mean dist 0.5 [1.4 (%10.0)->0.7 (%90.0))]
%58 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=mercu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.25 (0.09-->6.18) (max @ vno 77416 --> 72693)
face area 0.33 +- 0.15 (0.00-->3.20)
mean absolute distance = 0.40 +- 0.64
2887 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2417453.2, rms=7.772
001: dt: 0.5000, sse=1314985.6, rms=4.672 (39.888%)
002: dt: 0.5000, sse=946534.4, rms=3.005 (35.679%)
003: dt: 0.5000, sse=843438.1, rms=2.331 (22.436%)
004: dt: 0.5000, sse=803290.6, rms=2.025 (13.096%)
rms = 2.01, time step reduction 1 of 3 to 0.250...
005: dt: 0.5000, sse=802372.8, rms=2.013 (0.594%)
006: dt: 0.2500, sse=748273.2, rms=1.364 (32.253%)
007: dt: 0.2500, sse=741220.8, rms=1.251 (8.263%)
rms = 1.22, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=738975.6, rms=1.220 (2.526%)
rms = 1.20, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=737641.1, rms=1.197 (1.838%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 26 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 3 with 40 points - only 0.00% unknown
deleting segment 4 with 43 points - only 0.00% unknown
deleting segment 5 with 66 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
deleting segment 7 with 25 points - only 40.00% unknown
deleting segment 8 with 6 points - only 0.00% unknown
mean border=88.9, 42 (13) missing vertices, mean dist -0.3 [0.5 (%71.9)->0.2 (%28.1))]
%72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=mercu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.24 (0.07-->6.43) (max @ vno 77416 --> 72693)
face area 0.35 +- 0.16 (0.00-->3.81)
mean absolute distance = 0.29 +- 0.41
4611 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1255900.8, rms=4.181
010: dt: 0.5000, sse=950096.5, rms=2.606 (37.675%)
011: dt: 0.5000, sse=873198.8, rms=2.040 (21.722%)
012: dt: 0.5000, sse=845106.9, rms=1.794 (12.038%)
rms = 1.85, time step reduction 1 of 3 to 0.250...
013: dt: 0.2500, sse=809533.8, rms=1.348 (24.873%)
014: dt: 0.2500, sse=792718.1, rms=1.078 (20.014%)
015: dt: 0.2500, sse=789160.9, rms=1.019 (5.508%)
rms = 1.01, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=788843.6, rms=1.010 (0.833%)
rms = 1.00, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=787955.8, rms=1.000 (1.058%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 25 points - only 0.00% unknown
deleting segment 1 with 45 points - only 0.00% unknown
deleting segment 2 with 49 points - only 0.00% unknown
deleting segment 3 with 85 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 4 points - only 0.00% unknown
deleting segment 5 with 25 points - only 40.00% unknown
deleting segment 6 with 6 points - only 0.00% unknown
mean border=91.5, 31 (5) missing vertices, mean dist -0.2 [0.3 (%77.3)->0.2 (%22.7))]
%85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=mercu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.25 (0.07-->6.59) (max @ vno 77416 --> 72693)
face area 0.34 +- 0.16 (0.00-->3.82)
mean absolute distance = 0.21 +- 0.31
4020 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1039262.9, rms=3.330
018: dt: 0.5000, sse=825918.1, rms=1.842 (44.672%)
019: dt: 0.5000, sse=812993.2, rms=1.736 (5.758%)
rms = 1.70, time step reduction 1 of 3 to 0.250...
020: dt: 0.5000, sse=807863.8, rms=1.702 (1.978%)
021: dt: 0.2500, sse=758106.8, rms=1.034 (39.225%)
022: dt: 0.2500, sse=752724.0, rms=0.942 (8.948%)
rms = 0.94, time step reduction 2 of 3 to 0.125...
rms = 0.93, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=751912.7, rms=0.932 (1.024%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 25 points - only 0.00% unknown
deleting segment 1 with 45 points - only 0.00% unknown
deleting segment 2 with 63 points - only 0.00% unknown
deleting segment 3 with 77 points - only 0.00% unknown
deleting segment 4 with 7 points - only 0.00% unknown
deleting segment 5 with 25 points - only 40.00% unknown
deleting segment 6 with 6 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 points - only 0.00% unknown
mean border=92.4, 28 (1) missing vertices, mean dist -0.1 [0.2 (%60.5)->0.2 (%39.5))]
%90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=mercu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=769808.0, rms=1.450
024: dt: 0.5000, sse=751505.6, rms=1.150 (20.713%)
rms = 1.47, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=732050.4, rms=0.842 (26.783%)
026: dt: 0.2500, sse=728140.2, rms=0.763 (9.375%)
rms = 0.74, time step reduction 2 of 3 to 0.125...
027: dt: 0.2500, sse=725545.0, rms=0.738 (3.259%)
rms = 0.73, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=724683.1, rms=0.732 (0.856%)
positioning took 0.5 minutes
generating cortex label...
12 non-cortical segments detected
only using segment with 7801 vertices
erasing segment 1 (vno[0] = 58973)
erasing segment 2 (vno[0] = 105604)
erasing segment 3 (vno[0] = 107751)
erasing segment 4 (vno[0] = 108658)
erasing segment 5 (vno[0] = 108689)
erasing segment 6 (vno[0] = 109508)
erasing segment 7 (vno[0] = 109569)
erasing segment 8 (vno[0] = 111718)
erasing segment 9 (vno[0] = 112671)
erasing segment 10 (vno[0] = 116519)
erasing segment 11 (vno[0] = 116533)
writing cortex label to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/lh.cortex.label...
writing curvature file /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.area
vertex spacing 0.88 +- 0.25 (0.01-->6.66) (max @ vno 72693 --> 77416)
face area 0.33 +- 0.16 (0.00-->3.77)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 0 with 2 points - only 0.00% unknown
deleting segment 3 with 21 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=64.6, 58 (58) missing vertices, mean dist 1.8 [0.4 (%0.0)->2.7 (%100.0))]
%17 local maxima, %46 large gradients and %33 min vals, 216 gradients ignored
perforing initial smooth deformation to move away from white surface
tol=1.0e-04, sigma=2.0, host=mercu, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.05
000: dt: 0.0000, sse=23832664.0, rms=28.525
001: dt: 0.0500, sse=21448394.0, rms=27.016 (5.291%)
002: dt: 0.0500, sse=19747196.0, rms=25.885 (4.186%)
003: dt: 0.0500, sse=18444834.0, rms=24.985 (3.478%)
004: dt: 0.0500, sse=17390262.0, rms=24.231 (3.017%)
005: dt: 0.0500, sse=16500629.0, rms=23.576 (2.701%)
006: dt: 0.0500, sse=15726664.0, rms=22.992 (2.480%)
007: dt: 0.0500, sse=15038625.0, rms=22.459 (2.317%)
008: dt: 0.0500, sse=14416848.0, rms=21.967 (2.193%)
009: dt: 0.0500, sse=13847906.0, rms=21.506 (2.097%)
010: dt: 0.0500, sse=13321672.0, rms=21.071 (2.023%)
positioning took 0.8 minutes
mean border=64.5, 53 (34) missing vertices, mean dist 1.4 [0.2 (%0.0)->2.2 (%100.0))]
%18 local maxima, %46 large gradients and %32 min vals, 202 gradients ignored
tol=1.0e-04, sigma=2.0, host=mercu, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.05
000: dt: 0.0000, sse=14071028.0, rms=21.688
011: dt: 0.0500, sse=13579509.0, rms=21.286 (1.856%)
012: dt: 0.0500, sse=13119140.0, rms=20.902 (1.805%)
013: dt: 0.0500, sse=12686227.0, rms=20.534 (1.760%)
014: dt: 0.0500, sse=12277557.0, rms=20.180 (1.721%)
015: dt: 0.0500, sse=11890917.0, rms=19.840 (1.686%)
016: dt: 0.0500, sse=11524486.0, rms=19.512 (1.653%)
017: dt: 0.0500, sse=11176655.0, rms=19.195 (1.623%)
018: dt: 0.0500, sse=10846317.0, rms=18.890 (1.592%)
019: dt: 0.0500, sse=10532304.0, rms=18.595 (1.563%)
020: dt: 0.0500, sse=10233729.0, rms=18.309 (1.534%)
positioning took 0.8 minutes
mean border=64.3, 59 (22) missing vertices, mean dist 1.2 [0.1 (%0.3)->1.8 (%99.7))]
%18 local maxima, %46 large gradients and %32 min vals, 193 gradients ignored
tol=1.0e-04, sigma=2.0, host=mercu, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.05
000: dt: 0.0000, sse=10359275.0, rms=18.434
021: dt: 0.0500, sse=10070248.0, rms=18.156 (1.511%)
022: dt: 0.0500, sse=9795212.0, rms=17.887 (1.482%)
023: dt: 0.0500, sse=9532534.0, rms=17.626 (1.459%)
024: dt: 0.0500, sse=9282515.0, rms=17.374 (1.430%)
025: dt: 0.0500, sse=9044150.0, rms=17.130 (1.404%)
026: dt: 0.0500, sse=8816715.0, rms=16.894 (1.378%)
027: dt: 0.0500, sse=8598265.0, rms=16.664 (1.361%)
028: dt: 0.0500, sse=8386920.0, rms=16.438 (1.354%)
029: dt: 0.0500, sse=8182366.0, rms=16.217 (1.347%)
030: dt: 0.0500, sse=7984147.5, rms=15.999 (1.341%)
positioning took 0.8 minutes
mean border=64.2, 74 (21) missing vertices, mean dist 1.0 [0.1 (%5.4)->1.6 (%94.6))]
%18 local maxima, %46 large gradients and %31 min vals, 176 gradients ignored
tol=1.0e-04, sigma=2.0, host=mercu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 1.000
averaging target values for 5 iterations...
000: dt: 0.0000, sse=8077352.0, rms=16.102
031: dt: 0.5000, sse=6644939.5, rms=14.445 (10.293%)
032: dt: 0.5000, sse=5536837.5, rms=13.013 (9.908%)
033: dt: 0.5000, sse=4596311.5, rms=11.664 (10.368%)
034: dt: 0.5000, sse=3783920.0, rms=10.353 (11.244%)
035: dt: 0.5000, sse=3071721.5, rms=9.052 (12.564%)
036: dt: 0.5000, sse=2483297.5, rms=7.811 (13.710%)
037: dt: 0.5000, sse=2019062.0, rms=6.677 (14.520%)
038: dt: 0.5000, sse=1708558.9, rms=5.790 (13.277%)
039: dt: 0.5000, sse=1517869.1, rms=5.176 (10.606%)
040: dt: 0.5000, sse=1418576.1, rms=4.821 (6.870%)
041: dt: 0.5000, sse=1356598.8, rms=4.591 (4.769%)
042: dt: 0.5000, sse=1328094.6, rms=4.474 (2.547%)
043: dt: 0.5000, sse=1305685.6, rms=4.387 (1.933%)
rms = 4.35, time step reduction 1 of 3 to 0.250...
044: dt: 0.5000, sse=1296914.6, rms=4.347 (0.908%)
045: dt: 0.2500, sse=1144676.4, rms=3.611 (16.931%)
046: dt: 0.2500, sse=1108058.0, rms=3.423 (5.217%)
rms = 3.41, time step reduction 2 of 3 to 0.125...
047: dt: 0.2500, sse=1106823.9, rms=3.412 (0.332%)
048: dt: 0.1250, sse=1081809.0, rms=3.272 (4.085%)
rms = 3.25, time step reduction 3 of 3 to 0.062...
049: dt: 0.1250, sse=1078729.1, rms=3.255 (0.528%)
positioning took 1.9 minutes
mean border=62.9, 1841 (11) missing vertices, mean dist 0.1 [0.2 (%44.5)->0.4 (%55.5))]
%35 local maxima, %32 large gradients and %28 min vals, 86 gradients ignored
tol=1.0e-04, sigma=1.0, host=mercu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1422618.6, rms=4.067
050: dt: 0.5000, sse=1360840.4, rms=3.801 (6.553%)
051: dt: 0.5000, sse=1334764.6, rms=3.717 (2.218%)
rms = 3.91, time step reduction 1 of 3 to 0.250...
052: dt: 0.2500, sse=1193105.6, rms=2.904 (21.850%)
053: dt: 0.2500, sse=1151672.1, rms=2.616 (9.914%)
rms = 2.57, time step reduction 2 of 3 to 0.125...
054: dt: 0.2500, sse=1145174.9, rms=2.572 (1.707%)
055: dt: 0.1250, sse=1120218.4, rms=2.381 (7.435%)
rms = 2.36, time step reduction 3 of 3 to 0.062...
056: dt: 0.1250, sse=1116829.2, rms=2.356 (1.036%)
positioning took 0.9 minutes
mean border=61.9, 1970 (10) missing vertices, mean dist 0.1 [0.1 (%42.9)->0.3 (%57.1))]
%48 local maxima, %19 large gradients and %27 min vals, 137 gradients ignored
tol=1.0e-04, sigma=0.5, host=mercu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1192483.4, rms=2.873
rms = 3.33, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1138085.2, rms=2.505 (12.789%)
058: dt: 0.2500, sse=1122271.2, rms=2.390 (4.591%)
rms = 2.37, time step reduction 2 of 3 to 0.125...
059: dt: 0.2500, sse=1118236.6, rms=2.371 (0.830%)
060: dt: 0.1250, sse=1109511.6, rms=2.298 (3.060%)
rms = 2.29, time step reduction 3 of 3 to 0.062...
061: dt: 0.1250, sse=1107643.8, rms=2.286 (0.520%)
positioning took 0.7 minutes
mean border=61.3, 3710 (10) missing vertices, mean dist 0.0 [0.1 (%46.4)->0.2 (%53.6))]
%52 local maxima, %15 large gradients and %26 min vals, 123 gradients ignored
tol=1.0e-04, sigma=0.2, host=mercu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing pial surface to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1125937.0, rms=2.424
rms = 2.84, time step reduction 1 of 3 to 0.250...
062: dt: 0.2500, sse=1109252.4, rms=2.292 (5.431%)
rms = 2.26, time step reduction 2 of 3 to 0.125...
063: dt: 0.2500, sse=1103471.1, rms=2.258 (1.475%)
rms = 2.21, time step reduction 3 of 3 to 0.062...
064: dt: 0.1250, sse=1098387.8, rms=2.213 (1.993%)
positioning took 0.5 minutes
writing curvature file /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.area.pial
vertex spacing 0.99 +- 0.41 (0.06-->6.59) (max @ vno 101531 --> 100471)
face area 0.39 +- 0.29 (0.00-->6.57)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 148761 vertices processed
25000 of 148761 vertices processed
50000 of 148761 vertices processed
75000 of 148761 vertices processed
100000 of 148761 vertices processed
125000 of 148761 vertices processed
0 of 148761 vertices processed
25000 of 148761 vertices processed
50000 of 148761 vertices processed
75000 of 148761 vertices processed
100000 of 148761 vertices processed
125000 of 148761 vertices processed
thickness calculation complete, 277:678 truncations.
40077 vertices at 0 distance
111809 vertices at 1 distance
84682 vertices at 2 distance
32955 vertices at 3 distance
10179 vertices at 4 distance
3024 vertices at 5 distance
935 vertices at 6 distance
353 vertices at 7 distance
150 vertices at 8 distance
78 vertices at 9 distance
53 vertices at 10 distance
36 vertices at 11 distance
26 vertices at 12 distance
19 vertices at 13 distance
13 vertices at 14 distance
13 vertices at 15 distance
5 vertices at 16 distance
2 vertices at 17 distance
5 vertices at 18 distance
2 vertices at 19 distance
2 vertices at 20 distance
writing curvature file /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.thickness
positioning took 12.2 minutes
#--------------------------------------------
#@# Make Pial Surf rh Mon Feb 15 23:50:40 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs stripped rh 

using white.preaparc starting white location...
using white.preaparc starting pial locations...
using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline
INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $
$Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/filled.mgz...
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/brain.finalsurfs.mgz...
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/../mri/aseg.presurf.mgz...
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/wm.mgz...
26904 bright wm thresholded.
515 bright non-wm voxels segmented.
reading original surface position from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.orig...
computing class statistics...
border white:    280914 voxels (1.67%)
border gray      308996 voxels (1.84%)
WM (102.0): 101.5 +- 6.8 [70.0 --> 110.0]
GM (80.0) : 79.2 +- 10.2 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 67.8 (was 70)
setting MAX_BORDER_WHITE to 112.8 (was 105)
setting MIN_BORDER_WHITE to 78.0 (was 85)
setting MAX_CSF to 57.5 (was 40)
setting MAX_GRAY to 99.2 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 67.8 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 47.3 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106+-4.3,    GM=78+-6.1
mean inside = 98.0, mean outside = 82.6
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.88 +- 0.24 (0.04-->3.45) (max @ vno 81042 --> 151272)
face area 0.33 +- 0.15 (0.00-->2.77)
mean absolute distance = 0.71 +- 0.91
2675 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
deleting segment 2 with 12 points - only 0.00% unknown
deleting segment 3 with 98 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 4 with 1 points - only 0.00% unknown
deleting segment 5 with 41 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 6 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 points - only 0.00% unknown
mean border=86.6, 49 (49) missing vertices, mean dist 0.4 [1.3 (%10.5)->0.6 (%89.5))]
%57 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=mercu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.25 (0.12-->3.72) (max @ vno 151272 --> 81042)
face area 0.33 +- 0.15 (0.00-->2.61)
mean absolute distance = 0.37 +- 0.61
2677 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2302630.5, rms=7.409
001: dt: 0.5000, sse=1275724.1, rms=4.432 (40.184%)
002: dt: 0.5000, sse=941380.7, rms=2.870 (35.236%)
003: dt: 0.5000, sse=850353.5, rms=2.283 (20.463%)
004: dt: 0.5000, sse=816060.3, rms=2.012 (11.852%)
rms = 2.03, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=778232.9, rms=1.591 (20.928%)
006: dt: 0.2500, sse=760854.0, rms=1.358 (14.633%)
007: dt: 0.2500, sse=755560.4, rms=1.281 (5.715%)
rms = 1.24, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=752933.0, rms=1.240 (3.200%)
rms = 1.21, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=751956.3, rms=1.215 (2.027%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 30 points - only 0.00% unknown
deleting segment 1 with 54 points - only 0.00% unknown
deleting segment 2 with 41 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 2 points - only 0.00% unknown
mean border=89.3, 6 (2) missing vertices, mean dist -0.2 [0.4 (%70.4)->0.2 (%29.6))]
%70 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=mercu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.24 (0.10-->3.91) (max @ vno 107193 --> 107213)
face area 0.35 +- 0.16 (0.00-->3.03)
mean absolute distance = 0.29 +- 0.40
4704 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1227937.4, rms=3.979
010: dt: 0.5000, sse=933503.7, rms=2.402 (39.643%)
011: dt: 0.5000, sse=868793.6, rms=1.899 (20.917%)
012: dt: 0.5000, sse=850703.9, rms=1.745 (8.100%)
rms = 1.85, time step reduction 1 of 3 to 0.250...
013: dt: 0.2500, sse=814413.9, rms=1.282 (26.549%)
014: dt: 0.2500, sse=799770.6, rms=1.043 (18.632%)
rms = 1.01, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=797780.1, rms=1.008 (3.333%)
rms = 1.00, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=797244.7, rms=0.995 (1.300%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 28 points - only 0.00% unknown
deleting segment 1 with 6 points - only 0.00% unknown
deleting segment 2 with 68 points - only 0.00% unknown
deleting segment 3 with 41 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 5 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 6 with 1 points - only 0.00% unknown
mean border=91.8, 12 (1) missing vertices, mean dist -0.2 [0.3 (%76.0)->0.2 (%24.0))]
%84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=mercu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.24 (0.11-->3.93) (max @ vno 79330 --> 79331)
face area 0.34 +- 0.16 (0.00-->3.23)
mean absolute distance = 0.21 +- 0.31
3807 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1033892.7, rms=3.198
017: dt: 0.5000, sse=846033.6, rms=1.890 (40.896%)
018: dt: 0.5000, sse=830044.2, rms=1.759 (6.940%)
rms = 1.72, time step reduction 1 of 3 to 0.250...
019: dt: 0.5000, sse=823532.4, rms=1.719 (2.294%)
020: dt: 0.2500, sse=772291.1, rms=1.047 (39.112%)
021: dt: 0.2500, sse=766894.4, rms=0.951 (9.178%)
rms = 0.95, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=767323.7, rms=0.950 (0.098%)
rms = 0.93, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=765382.0, rms=0.934 (1.680%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 135 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
deleting segment 2 with 40 points - only 0.00% unknown
deleting segment 3 with 6 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
mean border=92.7, 13 (0) missing vertices, mean dist -0.1 [0.2 (%60.0)->0.2 (%40.0))]
%88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=mercu, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=779610.8, rms=1.411
024: dt: 0.5000, sse=757458.1, rms=1.074 (23.926%)
rms = 1.37, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=742889.4, rms=0.822 (23.483%)
026: dt: 0.2500, sse=739963.8, rms=0.761 (7.398%)
rms = 0.73, time step reduction 2 of 3 to 0.125...
027: dt: 0.2500, sse=737990.9, rms=0.734 (3.546%)
rms = 0.73, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=737075.1, rms=0.734 (-0.083%)
positioning took 0.5 minutes
generating cortex label...
9 non-cortical segments detected
only using segment with 7641 vertices
erasing segment 1 (vno[0] = 60982)
erasing segment 2 (vno[0] = 62551)
erasing segment 3 (vno[0] = 107158)
erasing segment 4 (vno[0] = 108219)
erasing segment 5 (vno[0] = 109279)
erasing segment 6 (vno[0] = 111474)
erasing segment 7 (vno[0] = 111492)
erasing segment 8 (vno[0] = 117283)
writing cortex label to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/rh.cortex.label...
writing curvature file /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.area
vertex spacing 0.88 +- 0.25 (0.05-->4.02) (max @ vno 81042 --> 151272)
face area 0.33 +- 0.16 (0.00-->3.02)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 1 with 5 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 3 with 28 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 18 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 8 with 4 points - only 0.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=65.3, 59 (59) missing vertices, mean dist 1.8 [0.8 (%0.0)->2.6 (%100.0))]
%18 local maxima, %47 large gradients and %31 min vals, 299 gradients ignored
perforing initial smooth deformation to move away from white surface
tol=1.0e-04, sigma=2.0, host=mercu, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.05
000: dt: 0.0000, sse=23516210.0, rms=28.052
001: dt: 0.0500, sse=21142678.0, rms=26.552 (5.345%)
002: dt: 0.0500, sse=19449900.0, rms=25.429 (4.231%)
003: dt: 0.0500, sse=18154070.0, rms=24.534 (3.519%)
004: dt: 0.0500, sse=17102928.0, rms=23.784 (3.060%)
005: dt: 0.0500, sse=16214838.0, rms=23.130 (2.747%)
006: dt: 0.0500, sse=15442410.0, rms=22.547 (2.523%)
007: dt: 0.0500, sse=14755675.0, rms=22.015 (2.359%)
008: dt: 0.0500, sse=14135442.0, rms=21.523 (2.234%)
009: dt: 0.0500, sse=13567854.0, rms=21.063 (2.138%)
010: dt: 0.0500, sse=13043929.0, rms=20.629 (2.060%)
positioning took 0.8 minutes
mean border=65.2, 40 (32) missing vertices, mean dist 1.4 [0.1 (%0.0)->2.1 (%100.0))]
%19 local maxima, %47 large gradients and %30 min vals, 265 gradients ignored
tol=1.0e-04, sigma=2.0, host=mercu, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.05
000: dt: 0.0000, sse=13859301.0, rms=21.301
011: dt: 0.0500, sse=13369435.0, rms=20.900 (1.881%)
012: dt: 0.0500, sse=12911552.0, rms=20.518 (1.826%)
013: dt: 0.0500, sse=12481518.0, rms=20.153 (1.780%)
014: dt: 0.0500, sse=12076579.0, rms=19.803 (1.737%)
015: dt: 0.0500, sse=11694430.0, rms=19.467 (1.698%)
016: dt: 0.0500, sse=11333217.0, rms=19.144 (1.661%)
017: dt: 0.0500, sse=10991539.0, rms=18.833 (1.624%)
018: dt: 0.0500, sse=10668095.0, rms=18.534 (1.589%)
019: dt: 0.0500, sse=10361370.0, rms=18.245 (1.556%)
020: dt: 0.0500, sse=10070530.0, rms=17.967 (1.523%)
positioning took 0.8 minutes
mean border=65.0, 41 (19) missing vertices, mean dist 1.2 [0.1 (%0.4)->1.8 (%99.6))]
%19 local maxima, %47 large gradients and %29 min vals, 265 gradients ignored
tol=1.0e-04, sigma=2.0, host=mercu, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.05
000: dt: 0.0000, sse=10212046.0, rms=18.108
021: dt: 0.0500, sse=9928974.0, rms=17.835 (1.505%)
022: dt: 0.0500, sse=9660203.0, rms=17.573 (1.473%)
023: dt: 0.0500, sse=9403641.0, rms=17.318 (1.448%)
024: dt: 0.0500, sse=9159723.0, rms=17.073 (1.418%)
025: dt: 0.0500, sse=8927498.0, rms=16.835 (1.389%)
026: dt: 0.0500, sse=8706031.0, rms=16.606 (1.363%)
027: dt: 0.0500, sse=8493159.0, rms=16.382 (1.347%)
028: dt: 0.0500, sse=8286555.0, rms=16.162 (1.343%)
029: dt: 0.0500, sse=8085971.5, rms=15.946 (1.340%)
030: dt: 0.0500, sse=7890817.0, rms=15.732 (1.340%)
positioning took 0.8 minutes
mean border=64.9, 53 (15) missing vertices, mean dist 1.0 [0.1 (%6.8)->1.5 (%93.2))]
%19 local maxima, %47 large gradients and %29 min vals, 241 gradients ignored
tol=1.0e-04, sigma=2.0, host=mercu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 1.000
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7989321.5, rms=15.840
031: dt: 0.5000, sse=6550560.5, rms=14.178 (10.492%)
032: dt: 0.5000, sse=5423297.0, rms=12.719 (10.287%)
033: dt: 0.5000, sse=4468944.5, rms=11.342 (10.831%)
034: dt: 0.5000, sse=3653526.2, rms=10.009 (11.748%)
035: dt: 0.5000, sse=2974703.8, rms=8.749 (12.588%)
036: dt: 0.5000, sse=2424176.5, rms=7.571 (13.468%)
037: dt: 0.5000, sse=1992221.9, rms=6.505 (14.083%)
038: dt: 0.5000, sse=1700061.8, rms=5.664 (12.917%)
039: dt: 0.5000, sse=1516432.4, rms=5.072 (10.453%)
040: dt: 0.5000, sse=1421313.9, rms=4.728 (6.788%)
041: dt: 0.5000, sse=1359074.2, rms=4.497 (4.878%)
042: dt: 0.5000, sse=1327746.9, rms=4.367 (2.907%)
043: dt: 0.5000, sse=1302687.6, rms=4.271 (2.198%)
rms = 4.22, time step reduction 1 of 3 to 0.250...
044: dt: 0.5000, sse=1293040.0, rms=4.223 (1.113%)
045: dt: 0.2500, sse=1140169.9, rms=3.477 (17.665%)
046: dt: 0.2500, sse=1104053.4, rms=3.286 (5.489%)
rms = 3.27, time step reduction 2 of 3 to 0.125...
047: dt: 0.2500, sse=1101373.9, rms=3.267 (0.575%)
048: dt: 0.1250, sse=1076700.9, rms=3.126 (4.326%)
rms = 3.11, time step reduction 3 of 3 to 0.062...
049: dt: 0.1250, sse=1073783.5, rms=3.109 (0.532%)
positioning took 1.9 minutes
mean border=63.4, 1581 (2) missing vertices, mean dist 0.1 [0.2 (%43.9)->0.4 (%56.1))]
%37 local maxima, %32 large gradients and %26 min vals, 107 gradients ignored
tol=1.0e-04, sigma=1.0, host=mercu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1472987.2, rms=4.137
050: dt: 0.5000, sse=1398122.4, rms=3.823 (7.604%)
051: dt: 0.5000, sse=1360292.9, rms=3.678 (3.782%)
rms = 3.89, time step reduction 1 of 3 to 0.250...
052: dt: 0.2500, sse=1216972.5, rms=2.864 (22.149%)
053: dt: 0.2500, sse=1175826.6, rms=2.581 (9.853%)
rms = 2.55, time step reduction 2 of 3 to 0.125...
054: dt: 0.2500, sse=1171722.1, rms=2.551 (1.167%)
055: dt: 0.1250, sse=1146876.0, rms=2.364 (7.346%)
rms = 2.34, time step reduction 3 of 3 to 0.062...
056: dt: 0.1250, sse=1143949.2, rms=2.343 (0.873%)
positioning took 0.9 minutes
mean border=62.3, 1721 (1) missing vertices, mean dist 0.1 [0.1 (%40.8)->0.3 (%59.2))]
%51 local maxima, %19 large gradients and %25 min vals, 98 gradients ignored
tol=1.0e-04, sigma=0.5, host=mercu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1236105.5, rms=2.964
rms = 3.36, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1174893.9, rms=2.569 (13.320%)
058: dt: 0.2500, sse=1154286.4, rms=2.422 (5.730%)
rms = 2.39, time step reduction 2 of 3 to 0.125...
059: dt: 0.2500, sse=1148970.1, rms=2.393 (1.219%)
060: dt: 0.1250, sse=1138803.8, rms=2.311 (3.403%)
rms = 2.29, time step reduction 3 of 3 to 0.062...
061: dt: 0.1250, sse=1136291.9, rms=2.295 (0.714%)
positioning took 0.7 minutes
mean border=61.7, 3322 (1) missing vertices, mean dist 0.0 [0.2 (%44.5)->0.2 (%55.5))]
%55 local maxima, %14 large gradients and %24 min vals, 87 gradients ignored
tol=1.0e-04, sigma=0.2, host=mercu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing pial surface to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1155022.4, rms=2.438
rms = 2.85, time step reduction 1 of 3 to 0.250...
062: dt: 0.2500, sse=1135763.8, rms=2.290 (6.092%)
rms = 2.24, time step reduction 2 of 3 to 0.125...
063: dt: 0.2500, sse=1128030.2, rms=2.241 (2.147%)
064: dt: 0.1250, sse=1121977.9, rms=2.189 (2.302%)
rms = 2.17, time step reduction 3 of 3 to 0.062...
065: dt: 0.1250, sse=1119099.4, rms=2.171 (0.818%)
positioning took 0.6 minutes
writing curvature file /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.area.pial
vertex spacing 1.00 +- 0.41 (0.07-->7.89) (max @ vno 101084 --> 100008)
face area 0.39 +- 0.29 (0.00-->7.52)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 151498 vertices processed
25000 of 151498 vertices processed
50000 of 151498 vertices processed
75000 of 151498 vertices processed
100000 of 151498 vertices processed
125000 of 151498 vertices processed
150000 of 151498 vertices processed
0 of 151498 vertices processed
25000 of 151498 vertices processed
50000 of 151498 vertices processed
75000 of 151498 vertices processed
100000 of 151498 vertices processed
125000 of 151498 vertices processed
150000 of 151498 vertices processed
thickness calculation complete, 190:676 truncations.
41179 vertices at 0 distance
115118 vertices at 1 distance
86663 vertices at 2 distance
32817 vertices at 3 distance
9907 vertices at 4 distance
2874 vertices at 5 distance
863 vertices at 6 distance
254 vertices at 7 distance
93 vertices at 8 distance
36 vertices at 9 distance
22 vertices at 10 distance
22 vertices at 11 distance
11 vertices at 12 distance
13 vertices at 13 distance
8 vertices at 14 distance
7 vertices at 15 distance
11 vertices at 16 distance
10 vertices at 17 distance
6 vertices at 18 distance
7 vertices at 19 distance
17 vertices at 20 distance
writing curvature file /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.thickness
positioning took 12.4 minutes
#--------------------------------------------
#@# Surf Volume lh Tue Feb 16 00:03:03 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf
mris_calc -o lh.area.mid lh.area add lh.area.pial
Saving result to 'lh.area.mid' (type = MRI_CURV_FILE)                       [ ok ]
mris_calc -o lh.area.mid lh.area.mid div 2
Saving result to 'lh.area.mid' (type = MRI_CURV_FILE)                       [ ok ]
mris_convert --volume stripped lh /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.volume
masking with /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/lh.cortex.label
Total face volume 265930
Total vertex volume 262159 (mask=0)
#@# stripped lh 262159
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Tue Feb 16 00:03:07 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf
mris_calc -o rh.area.mid rh.area add rh.area.pial
Saving result to 'rh.area.mid' (type = MRI_CURV_FILE)                       [ ok ]
mris_calc -o rh.area.mid rh.area.mid div 2
Saving result to 'rh.area.mid' (type = MRI_CURV_FILE)                       [ ok ]
mris_convert --volume stripped rh /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.volume
masking with /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/rh.cortex.label
Total face volume 269042
Total vertex volume 265501 (mask=0)
#@# stripped rh 265501
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Tue Feb 16 00:03:10 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri

 mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon stripped 

SUBJECTS_DIR is /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
loading input data...
computing distance to left white surface 
computing distance to left pial surface 
computing distance to right white surface 
computing distance to right pial surface 
 hemi masks overlap voxels = 72
writing volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/ribbon.mgz
mris_volmask took 8.46 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Tue Feb 16 00:11:38 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab stripped lh white 

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/wm.mgz...
reading input surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white...
reading input pial surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.pial...
reading input white surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 265930
Total vertex volume 262159 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1687151 mm^3    (det: 1.154671 )
lhCtxGM: 261706.960 261208.000  diff=  499.0  pctdiff= 0.191
rhCtxGM: 265429.723 264692.000  diff=  737.7  pctdiff= 0.278
lhCtxWM: 250863.377 251388.500  diff= -525.1  pctdiff=-0.209
rhCtxWM: 254486.522 254925.500  diff= -439.0  pctdiff=-0.172
SubCortGMVol  61088.000
SupraTentVol  1110388.583 (1108114.000) diff=2274.583 pctdiff=0.205
SupraTentVolNotVent  1095628.583 (1093354.000) diff=2274.583 pctdiff=0.208
BrainSegVol  1251126.000 (1247891.000) diff=3235.000 pctdiff=0.259
BrainSegVolNotVent  1232173.000 (1232231.583) diff=-58.583 pctdiff=-0.005
BrainSegVolNotVent  1232173.000
CerebellumVol 138605.000
VentChorVol   14760.000
3rd4th5thCSF   4193.000
CSFVol   958.000, OptChiasmVol   214.000
MaskVol 1726540.000
 1521   1046   2620  2.602 0.370     0.111     0.019       10     1.1  bankssts
 1116    726   2118  2.782 0.598     0.130     0.019       15     0.9  caudalanteriorcingulate
 3293   2178   6304  2.654 0.460     0.112     0.021       27     2.7  caudalmiddlefrontal
 2198   1431   2521  1.776 0.384     0.146     0.033       30     3.0  cuneus
 1153    835   4365  3.591 0.696     0.141     0.040       18     1.8  entorhinal
 4516   3074   9314  2.732 0.560     0.136     0.029       68     5.1  fusiform
 7483   5031  13392  2.405 0.460     0.130     0.025       99     7.8  inferiorparietal
 4500   3067  10127  2.811 0.586     0.131     0.035       64     6.7  inferiortemporal
 1486    914   2481  2.338 0.823     0.124     0.029       22     1.5  isthmuscingulate
 8264   5201  11841  2.103 0.517     0.141     0.031      114    10.3  lateraloccipital
 4022   2693   8077  2.782 0.551     0.135     0.031       60     5.1  lateralorbitofrontal
 4438   2870   6206  2.108 0.595     0.143     0.034       60     6.3  lingual
 2935   2005   5397  2.458 0.662     0.119     0.026       41     2.7  medialorbitofrontal
 5271   3294  12598  2.963 0.575     0.123     0.030       72     6.8  middletemporal
 1058    691   2412  3.058 0.615     0.125     0.027       11     1.1  parahippocampal
 2269   1452   3588  2.359 0.577     0.107     0.018       17     1.7  paracentral
 2538   1700   5621  2.821 0.481     0.113     0.021       27     2.1  parsopercularis
 1049    674   2523  2.865 0.530     0.133     0.025       19     1.1  parsorbitalis
 2084   1339   4116  2.755 0.443     0.119     0.025       22     2.1  parstriangularis
 1898   1257   1825  1.596 0.387     0.154     0.041       27     3.2  pericalcarine
 6716   4116   9406  2.087 0.582     0.107     0.023       60     6.6  postcentral
 2094   1373   3738  2.518 0.639     0.139     0.030       33     2.5  posteriorcingulate
 8066   4699  13356  2.631 0.576     0.103     0.022       64     7.0  precentral
 6560   4330  10840  2.322 0.472     0.125     0.024       78     6.3  precuneus
 1620   1086   3521  3.010 0.618     0.137     0.035       30     2.2  rostralanteriorcingulate
 8645   5693  16727  2.546 0.524     0.131     0.029      124     9.7  rostralmiddlefrontal
12542   8317  27535  2.886 0.570     0.122     0.026      134    13.0  superiorfrontal
 8717   5647  13208  2.119 0.446     0.120     0.022      101     7.4  superiorparietal
 7981   5268  16603  2.820 0.525     0.114     0.021       89     6.7  superiortemporal
 8732   5789  16599  2.592 0.538     0.123     0.023      103     8.3  supramarginal
  384    259   1087  3.064 0.337     0.173     0.043        9     0.6  frontalpole
  704    526   2736  3.473 0.747     0.172     0.066       18     2.1  temporalpole
 1025    608   1850  2.592 0.429     0.120     0.025       12     1.0  transversetemporal
 3530   2402   7457  3.102 0.827     0.108     0.026       27     3.4  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab stripped lh pial 

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/wm.mgz...
reading input surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.pial...
reading input pial surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.pial...
reading input white surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 265930
Total vertex volume 262159 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1687151 mm^3    (det: 1.154671 )
lhCtxGM: 261706.960 261208.000  diff=  499.0  pctdiff= 0.191
rhCtxGM: 265429.723 264692.000  diff=  737.7  pctdiff= 0.278
lhCtxWM: 250863.377 251388.500  diff= -525.1  pctdiff=-0.209
rhCtxWM: 254486.522 254925.500  diff= -439.0  pctdiff=-0.172
SubCortGMVol  61088.000
SupraTentVol  1110388.583 (1108114.000) diff=2274.583 pctdiff=0.205
SupraTentVolNotVent  1095628.583 (1093354.000) diff=2274.583 pctdiff=0.208
BrainSegVol  1251126.000 (1247891.000) diff=3235.000 pctdiff=0.259
BrainSegVolNotVent  1232173.000 (1232231.583) diff=-58.583 pctdiff=-0.005
BrainSegVolNotVent  1232173.000
CerebellumVol 138605.000
VentChorVol   14760.000
3rd4th5thCSF   4193.000
CSFVol   958.000, OptChiasmVol   214.000
MaskVol 1726540.000
 1521    991   2620  2.602 0.370     0.124     0.032       25     2.1  bankssts
 1116    858   2118  2.782 0.598     0.159     0.037       44     1.8  caudalanteriorcingulate
 3293   2445   6304  2.654 0.460     0.118     0.025       39     3.5  caudalmiddlefrontal
 2198   1508   2521  1.776 0.384     0.132     0.031       36     3.0  cuneus
 1153   1596   4365  3.591 0.696     0.196     0.037       12     2.2  entorhinal
 4516   3678   9314  2.732 0.560     0.144     0.034       67     7.1  fusiform
 7483   6099  13392  2.405 0.460     0.141     0.028       89     9.5  inferiorparietal
 4500   3891  10127  2.811 0.586     0.149     0.036       69     7.5  inferiortemporal
 1486   1150   2481  2.338 0.823     0.136     0.035       20     2.2  isthmuscingulate
 8264   6100  11841  2.103 0.517     0.130     0.031      115    11.1  lateraloccipital
 4022   3065   8077  2.782 0.551     0.131     0.032       68     5.7  lateralorbitofrontal
 4438   3219   6206  2.108 0.595     0.135     0.035       63     7.0  lingual
 2935   2379   5397  2.458 0.662     0.131     0.029       44     4.0  medialorbitofrontal
 5271   4913  12598  2.963 0.575     0.147     0.027       55     6.9  middletemporal
 1058    935   2412  3.058 0.615     0.147     0.033       13     1.6  parahippocampal
 2269   1642   3588  2.359 0.577     0.112     0.021       20     2.2  paracentral
 2538   2245   5621  2.821 0.481     0.140     0.027       27     3.2  parsopercularis
 1049   1049   2523  2.865 0.530     0.145     0.023       12     1.1  parsorbitalis
 2084   1592   4116  2.755 0.443     0.138     0.027       27     2.6  parstriangularis
 1898   1145   1825  1.596 0.387     0.124     0.034       33     2.7  pericalcarine
 6716   5008   9406  2.087 0.582     0.115     0.022       64     6.6  postcentral
 2094   1551   3738  2.518 0.639     0.151     0.039       55     3.5  posteriorcingulate
 8066   5381  13356  2.631 0.576     0.100     0.020       79     6.8  precentral
 6560   4939  10840  2.322 0.472     0.133     0.029       89     8.0  precuneus
 1620   1332   3521  3.010 0.618     0.136     0.031       22     2.0  rostralanteriorcingulate
 8645   7210  16727  2.546 0.524     0.147     0.030      110    11.5  rostralmiddlefrontal
12542  10301  27535  2.886 0.570     0.133     0.028      142    14.9  superiorfrontal
 8717   6664  13208  2.119 0.446     0.130     0.024       97     8.9  superiorparietal
 7981   6256  16603  2.820 0.525     0.126     0.028       91     9.8  superiortemporal
 8732   6783  16599  2.592 0.538     0.140     0.136     2019    85.3  supramarginal
  384    448   1087  3.064 0.337     0.196     0.029        4     0.6  frontalpole
  704    972   2736  3.473 0.747     0.250     0.054       33     2.1  temporalpole
 1025    880   1850  2.592 0.429     0.124     0.026        6     1.2  transversetemporal
 3530   2234   7457  3.102 0.827     0.122     0.036      129     5.6  insula
#-----------------------------------------
#@# Parcellation Stats rh Tue Feb 16 00:12:34 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab stripped rh white 

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/wm.mgz...
reading input surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white...
reading input pial surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.pial...
reading input white surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 269042
Total vertex volume 265501 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1687151 mm^3    (det: 1.154671 )
lhCtxGM: 261706.960 261208.000  diff=  499.0  pctdiff= 0.191
rhCtxGM: 265429.723 264692.000  diff=  737.7  pctdiff= 0.278
lhCtxWM: 250863.377 251388.500  diff= -525.1  pctdiff=-0.209
rhCtxWM: 254486.522 254925.500  diff= -439.0  pctdiff=-0.172
SubCortGMVol  61088.000
SupraTentVol  1110388.583 (1108114.000) diff=2274.583 pctdiff=0.205
SupraTentVolNotVent  1095628.583 (1093354.000) diff=2274.583 pctdiff=0.208
BrainSegVol  1251126.000 (1247891.000) diff=3235.000 pctdiff=0.259
BrainSegVolNotVent  1232173.000 (1232231.583) diff=-58.583 pctdiff=-0.005
BrainSegVolNotVent  1232173.000
CerebellumVol 138605.000
VentChorVol   14760.000
3rd4th5thCSF   4193.000
CSFVol   958.000, OptChiasmVol   214.000
MaskVol 1726540.000
 1334    907   2343  2.653 0.367     0.108     0.019       11     1.0  bankssts
  891    579   1660  2.837 0.524     0.131     0.015       14     0.6  caudalanteriorcingulate
 3710   2484   7522  2.685 0.447     0.123     0.025       38     3.9  caudalmiddlefrontal
 2470   1582   3201  1.869 0.430     0.139     0.028       31     2.9  cuneus
  737    503   2525  3.530 0.726     0.124     0.036        8     0.9  entorhinal
 5042   3377  10752  2.811 0.570     0.130     0.027       66     5.6  fusiform
 9815   6396  17289  2.458 0.503     0.127     0.024      129     9.7  inferiorparietal
 6509   4268  14166  2.872 0.640     0.127     0.029       87     7.5  inferiortemporal
 1466    918   2630  2.601 0.693     0.137     0.032       21     1.8  isthmuscingulate
 8226   5168  12009  2.127 0.543     0.133     0.027      107     8.8  lateraloccipital
 3659   2477   7108  2.540 0.583     0.138     0.033       56     4.9  lateralorbitofrontal
 4762   3159   6816  2.051 0.650     0.145     0.034       66     6.8  lingual
 3345   2308   6676  2.467 0.665     0.127     0.027       52     3.8  medialorbitofrontal
 6068   4075  13664  2.816 0.567     0.117     0.022       72     5.4  middletemporal
 1115    706   2334  2.804 0.649     0.112     0.024       11     1.0  parahippocampal
 2559   1657   4222  2.395 0.506     0.105     0.017       18     1.8  paracentral
 2261   1517   4764  2.808 0.515     0.111     0.021       23     1.9  parsopercularis
 1307    875   3113  2.769 0.721     0.139     0.028       23     1.4  parsorbitalis
 2166   1489   4397  2.650 0.490     0.123     0.028       27     2.4  parstriangularis
 2067   1327   2099  1.692 0.463     0.126     0.030       23     2.4  pericalcarine
 7219   4334   9960  2.127 0.611     0.113     0.022       74     6.7  postcentral
 1912   1305   3531  2.496 0.551     0.139     0.024       29     2.1  posteriorcingulate
 8646   5085  14213  2.594 0.547     0.100     0.021       68     7.9  precentral
 6403   4318  10992  2.417 0.509     0.137     0.029       87     7.5  precuneus
  884    607   2178  3.113 0.485     0.129     0.029       14     1.0  rostralanteriorcingulate
 9437   6347  17647  2.422 0.526     0.134     0.029      128    11.3  rostralmiddlefrontal
11443   7531  24597  2.829 0.545     0.117     0.026      114    11.5  superiorfrontal
 8963   5747  13535  2.139 0.466     0.129     0.025      117     9.1  superiorparietal
 6583   4335  14339  2.959 0.534     0.117     0.023       89     5.8  superiortemporal
 6811   4421  12619  2.641 0.493     0.124     0.025       82     6.9  supramarginal
  498    331   1234  2.722 0.451     0.171     0.042       11     0.9  frontalpole
  688    482   2618  3.766 0.591     0.148     0.049       11     1.3  temporalpole
  727    416   1370  2.685 0.283     0.116     0.020        8     0.5  transversetemporal
 3675   2495   7366  2.969 0.758     0.114     0.030       36     4.6  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab stripped rh pial 

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/wm.mgz...
reading input surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.pial...
reading input pial surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.pial...
reading input white surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 269042
Total vertex volume 265501 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1687151 mm^3    (det: 1.154671 )
lhCtxGM: 261706.960 261208.000  diff=  499.0  pctdiff= 0.191
rhCtxGM: 265429.723 264692.000  diff=  737.7  pctdiff= 0.278
lhCtxWM: 250863.377 251388.500  diff= -525.1  pctdiff=-0.209
rhCtxWM: 254486.522 254925.500  diff= -439.0  pctdiff=-0.172
SubCortGMVol  61088.000
SupraTentVol  1110388.583 (1108114.000) diff=2274.583 pctdiff=0.205
SupraTentVolNotVent  1095628.583 (1093354.000) diff=2274.583 pctdiff=0.208
BrainSegVol  1251126.000 (1247891.000) diff=3235.000 pctdiff=0.259
BrainSegVolNotVent  1232173.000 (1232231.583) diff=-58.583 pctdiff=-0.005
BrainSegVolNotVent  1232173.000
CerebellumVol 138605.000
VentChorVol   14760.000
3rd4th5thCSF   4193.000
CSFVol   958.000, OptChiasmVol   214.000
MaskVol 1726540.000
 1334    845   2343  2.653 0.367     0.120     0.031       16     1.7  bankssts
  891    675   1660  2.837 0.524     0.127     0.028       30     0.9  caudalanteriorcingulate
 3710   2990   7522  2.685 0.447     0.130     0.026       40     4.2  caudalmiddlefrontal
 2470   1942   3201  1.869 0.430     0.145     0.031       36     3.6  cuneus
  737    887   2525  3.530 0.726     0.190     0.041       14     1.4  entorhinal
 5042   4158  10752  2.811 0.570     0.144     0.033       75     7.6  fusiform
 9815   7579  17289  2.458 0.503     0.136     0.028      120    12.1  inferiorparietal
 6509   5426  14166  2.872 0.640     0.135     0.032      102     9.2  inferiortemporal
 1466   1082   2630  2.601 0.693     0.140     0.035       39     2.1  isthmuscingulate
 8226   6176  12009  2.127 0.543     0.129     0.028      127    10.6  lateraloccipital
 3659   3068   7108  2.540 0.583     0.170     0.039       61     6.7  lateralorbitofrontal
 4762   3606   6816  2.051 0.650     0.137     0.035       66     7.2  lingual
 3345   3038   6676  2.467 0.665     0.157     0.033       44     4.9  medialorbitofrontal
 6068   5520  13664  2.816 0.567     0.141     0.027       73     7.5  middletemporal
 1115    948   2334  2.804 0.649     0.136     0.030       13     1.5  parahippocampal
 2559   1835   4222  2.395 0.506     0.109     0.021       23     2.5  paracentral
 2261   1860   4764  2.808 0.515     0.131     0.025       24     2.5  parsopercularis
 1307   1324   3113  2.769 0.721     0.164     0.026       15     1.6  parsorbitalis
 2166   1817   4397  2.650 0.490     0.138     0.028       25     2.9  parstriangularis
 2067   1261   2099  1.692 0.463     0.114     0.029       38     2.5  pericalcarine
 7219   5138   9960  2.127 0.611     0.116     0.022       64     6.7  postcentral
 1912   1551   3531  2.496 0.551     0.163     0.035      121     3.0  posteriorcingulate
 8646   5728  14213  2.594 0.547     0.099     0.019       81     7.4  precentral
 6403   4779  10992  2.417 0.509     0.139     0.033       87     9.0  precuneus
  884    837   2178  3.113 0.485     0.159     0.038       16     1.6  rostralanteriorcingulate
 9437   7956  17647  2.422 0.526     0.153     0.035      124    15.3  rostralmiddlefrontal
11443   9380  24597  2.829 0.545     0.132     0.028      136    13.7  superiorfrontal
 8963   6869  13535  2.139 0.466     0.135     0.027      105     9.6  superiorparietal
 6583   5237  14339  2.959 0.534     0.127     0.028       80     7.5  superiortemporal
 6811   5044  12619  2.641 0.493     0.129     0.029       72     8.8  supramarginal
  498    557   1234  2.722 0.451     0.202     0.039        6     0.8  frontalpole
  688    877   2618  3.766 0.591     0.203     0.044       11     1.5  temporalpole
  727    585   1370  2.685 0.283     0.110     0.025        4     0.7  transversetemporal
 3675   2290   7366  2.969 0.758     0.125     0.032       52     5.2  insula
#-----------------------------------------
#@# Cortical Parc 2 lh Tue Feb 16 00:13:33 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 stripped lh ../surf/lh.sphere.reg /airflow/apps/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot 

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /airflow/apps/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 2.9   using min determinant for regularization = 0.086
0 singular and 762 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
16 labels changed using aseg
relabeling using gibbs priors...
000:   9530 changed, 148761 examined...
001:   2211 changed, 37284 examined...
002:    654 changed, 11649 examined...
003:    255 changed, 3635 examined...
004:    124 changed, 1440 examined...
005:     61 changed, 701 examined...
006:     35 changed, 335 examined...
007:     24 changed, 190 examined...
008:     13 changed, 117 examined...
009:      5 changed, 69 examined...
010:      3 changed, 29 examined...
011:      2 changed, 17 examined...
012:      3 changed, 15 examined...
013:      1 changed, 12 examined...
014:      0 changed, 5 examined...
1 labels changed using aseg
000: 245 total segments, 159 labels (2084 vertices) changed
001: 91 total segments, 6 labels (32 vertices) changed
002: 86 total segments, 1 labels (3 vertices) changed
003: 85 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 34 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1226 vertices marked for relabeling...
1226 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 15 seconds.
#-----------------------------------------
#@# Cortical Parc 2 rh Tue Feb 16 00:13:48 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 stripped rh ../surf/rh.sphere.reg /airflow/apps/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot 

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /airflow/apps/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 1.4   using min determinant for regularization = 0.020
0 singular and 719 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
27 labels changed using aseg
relabeling using gibbs priors...
000:   9715 changed, 151498 examined...
001:   2148 changed, 38226 examined...
002:    628 changed, 11424 examined...
003:    270 changed, 3589 examined...
004:    134 changed, 1574 examined...
005:     70 changed, 731 examined...
006:     41 changed, 380 examined...
007:     17 changed, 215 examined...
008:     13 changed, 109 examined...
009:      8 changed, 71 examined...
010:      0 changed, 38 examined...
26 labels changed using aseg
000: 285 total segments, 202 labels (2965 vertices) changed
001: 101 total segments, 18 labels (60 vertices) changed
002: 83 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 35 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1011 vertices marked for relabeling...
1011 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 15 seconds.
#-----------------------------------------
#@# Parcellation Stats 2 lh Tue Feb 16 00:14:04 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab stripped lh white 

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/wm.mgz...
reading input surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white...
reading input pial surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.pial...
reading input white surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 265930
Total vertex volume 262159 (mask=0)
reading colortable from annotation file...
colortable with 76 entries read (originally Simple_surface_labels2008.txt)
Saving annotation colortable ../label/aparc.annot.a2009s.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1687151 mm^3    (det: 1.154671 )
lhCtxGM: 261706.960 261208.000  diff=  499.0  pctdiff= 0.191
rhCtxGM: 265429.723 264692.000  diff=  737.7  pctdiff= 0.278
lhCtxWM: 250863.377 251388.500  diff= -525.1  pctdiff=-0.209
rhCtxWM: 254486.522 254925.500  diff= -439.0  pctdiff=-0.172
SubCortGMVol  61088.000
SupraTentVol  1110388.583 (1108114.000) diff=2274.583 pctdiff=0.205
SupraTentVolNotVent  1095628.583 (1093354.000) diff=2274.583 pctdiff=0.208
BrainSegVol  1251126.000 (1247891.000) diff=3235.000 pctdiff=0.259
BrainSegVolNotVent  1232173.000 (1232231.583) diff=-58.583 pctdiff=-0.005
BrainSegVolNotVent  1232173.000
CerebellumVol 138605.000
VentChorVol   14760.000
3rd4th5thCSF   4193.000
CSFVol   958.000, OptChiasmVol   214.000
MaskVol 1726540.000
 1355    903   2634  2.552 0.502     0.147     0.041       21     2.2  G&S_frontomargin
 2063   1365   3740  2.479 0.474     0.152     0.031       32     2.6  G&S_occipital_inf
 1708    976   2574  2.218 0.587     0.104     0.020       15     1.5  G&S_paracentral
 1559    998   3364  2.806 0.495     0.132     0.034       20     2.3  G&S_subcentral
  697    482   1698  2.708 0.608     0.176     0.046       18     1.2  G&S_transv_frontopol
 2646   1846   5689  2.899 0.536     0.138     0.032       40     3.3  G&S_cingul-Ant
 1341    948   2621  2.687 0.419     0.112     0.016       11     1.0  G&S_cingul-Mid-Ant
 1523   1060   2851  2.494 0.467     0.131     0.027       17     1.8  G&S_cingul-Mid-Post
  730    467   1855  3.077 0.469     0.158     0.047       14     1.2  G_cingul-Post-dorsal
  314    185    587  2.522 0.794     0.154     0.033        7     0.3  G_cingul-Post-ventral
 2077   1331   2625  1.787 0.424     0.153     0.038       31     3.4  G_cuneus
 1337    870   3806  3.165 0.482     0.130     0.026       21     1.4  G_front_inf-Opercular
  422    251   1135  3.108 0.326     0.127     0.024        6     0.4  G_front_inf-Orbital
 1437    874   3346  2.961 0.370     0.128     0.032       21     1.7  G_front_inf-Triangul
 4699   2978  10868  2.774 0.508     0.135     0.030       74     5.6  G_front_middle
 8394   5343  20148  3.040 0.550     0.125     0.028      103     9.1  G_front_sup
  612    400   1481  3.385 0.594     0.113     0.025        6     0.6  G_Ins_lg&S_cent_ins
  701    447   2286  3.764 0.681     0.099     0.030        7     0.8  G_insular_short
 2370   1474   4650  2.486 0.438     0.150     0.034       42     3.2  G_occipital_middle
 1442    900   2060  2.049 0.441     0.139     0.029       19     1.7  G_occipital_sup
 1769   1131   4134  2.866 0.570     0.152     0.042       40     2.7  G_oc-temp_lat-fusifor
 3032   1880   4140  1.946 0.562     0.150     0.039       47     4.9  G_oc-temp_med-Lingual
 1799   1240   6014  3.460 0.657     0.138     0.037       25     2.6  G_oc-temp_med-Parahip
 2665   1692   6424  2.910 0.584     0.144     0.036       57     3.7  G_orbital
 3497   2259   7574  2.592 0.486     0.139     0.031       64     4.2  G_pariet_inf-Angular
 3696   2391   8639  2.914 0.509     0.139     0.029       60     4.2  G_pariet_inf-Supramar
 3330   2113   6115  2.273 0.482     0.128     0.024       53     3.1  G_parietal_sup
 2668   1466   3658  2.078 0.471     0.107     0.023       26     2.6  G_postcentral
 3335   1562   5869  2.820 0.509     0.092     0.025       28     3.3  G_precentral
 3178   2030   6265  2.450 0.459     0.138     0.030       53     3.9  G_precuneus
 1061    709   2664  2.762 0.550     0.147     0.033       25     1.4  G_rectus
  888    597   1510  2.699 1.080     0.107     0.046       11     1.2  G_subcallosal
  759    434   1550  2.787 0.327     0.130     0.025       11     0.7  G_temp_sup-G_T_transv
 2795   1759   7315  3.055 0.573     0.130     0.026       48     2.7  G_temp_sup-Lateral
  729    535   2270  3.565 0.607     0.110     0.023        6     0.7  G_temp_sup-Plan_polar
 1903   1230   3574  2.615 0.451     0.101     0.019       16     1.3  G_temp_sup-Plan_tempo
 2512   1642   6356  2.871 0.577     0.139     0.039       47     4.2  G_temporal_inf
 3155   1855   8223  3.037 0.550     0.134     0.038       56     5.5  G_temporal_middle
  270    185    396  2.442 0.358     0.100     0.016        1     0.2  Lat_Fis-ant-Horizont
  426    302    692  2.531 0.399     0.093     0.012        2     0.3  Lat_Fis-ant-Vertical
 1436    973   1924  2.368 0.384     0.117     0.022       11     1.3  Lat_Fis-post
 2636   1543   2879  1.752 0.423     0.147     0.037       40     3.9  Pole_occipital
 1863   1316   6433  3.310 0.708     0.159     0.053       39     4.0  Pole_temporal
 2110   1443   2379  1.910 0.631     0.139     0.033       23     2.7  S_calcarine
 3170   2154   3623  1.941 0.542     0.106     0.019       20     2.5  S_central
 1243    853   1690  2.220 0.434     0.107     0.016        8     0.8  S_cingul-Marginalis
  522    354    806  3.015 0.513     0.110     0.021        3     0.5  S_circular_insula_ant
 1545   1096   2536  2.762 0.562     0.093     0.014        6     1.0  S_circular_insula_inf
 1749   1248   2664  2.563 0.371     0.110     0.018       10     1.3  S_circular_insula_sup
 1001    730   1667  2.571 0.400     0.109     0.017        8     0.7  S_collat_transv_ant
  601    405    756  2.040 0.391     0.145     0.034        6     0.8  S_collat_transv_post
 2308   1608   3881  2.437 0.422     0.108     0.018       17     1.5  S_front_inf
 1404    937   2088  2.209 0.431     0.123     0.026       16     1.4  S_front_middle
 3707   2538   6356  2.538 0.446     0.104     0.019       24     2.7  S_front_sup
  906    619   1139  2.195 0.399     0.104     0.014        6     0.6  S_interm_prim-Jensen
 3892   2605   4876  2.053 0.366     0.106     0.015       26     2.5  S_intrapariet&P_trans
 1116    738   1206  1.846 0.347     0.125     0.023       11     1.0  S_oc_middle&Lunatus
 1412    953   1768  2.082 0.371     0.114     0.019       12     1.1  S_oc_sup&transversal
  628    428    851  2.266 0.280     0.130     0.028        6     0.7  S_occipital_ant
  757    548   1318  2.465 0.431     0.111     0.015        4     0.5  S_oc-temp_lat
 2167   1514   3452  2.645 0.473     0.117     0.019       17     1.7  S_oc-temp_med&Lingual
  346    252    554  2.677 0.335     0.117     0.017        2     0.3  S_orbital_lateral
  680    481    968  2.391 0.507     0.121     0.019        5     0.5  S_orbital_med-olfact
 1484   1028   2716  2.653 0.486     0.134     0.028       19     1.6  S_orbital-H_Shaped
 2425   1607   3042  2.053 0.475     0.118     0.020       23     1.9  S_parieto_occipital
 1568    891   1426  2.120 0.856     0.120     0.018       25     0.9  S_pericallosal
 3333   2241   4513  2.111 0.420     0.103     0.018       24     2.5  S_postcentral
 1328    904   2049  2.532 0.388     0.096     0.013        6     0.7  S_precentral-inf-part
 1544   1086   2289  2.501 0.380     0.101     0.015        9     1.0  S_precentral-sup-part
  917    634   1226  2.163 0.507     0.105     0.013        6     0.6  S_suborbital
 1326    935   1892  2.204 0.381     0.115     0.020        9     1.0  S_subparietal
 1372    961   2070  2.671 0.446     0.117     0.020        9     1.2  S_temporal_inf
 6412   4448  10871  2.533 0.442     0.110     0.018       48     5.0  S_temporal_sup
  646    436    850  2.382 0.350     0.104     0.018        3     0.5  S_temporal_transverse
#-----------------------------------------
#@# Parcellation Stats 2 rh Tue Feb 16 00:14:35 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab stripped rh white 

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/wm.mgz...
reading input surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white...
reading input pial surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.pial...
reading input white surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 269042
Total vertex volume 265501 (mask=0)
reading colortable from annotation file...
colortable with 76 entries read (originally Simple_surface_labels2008.txt)
Saving annotation colortable ../label/aparc.annot.a2009s.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1687151 mm^3    (det: 1.154671 )
lhCtxGM: 261706.960 261208.000  diff=  499.0  pctdiff= 0.191
rhCtxGM: 265429.723 264692.000  diff=  737.7  pctdiff= 0.278
lhCtxWM: 250863.377 251388.500  diff= -525.1  pctdiff=-0.209
rhCtxWM: 254486.522 254925.500  diff= -439.0  pctdiff=-0.172
SubCortGMVol  61088.000
SupraTentVol  1110388.583 (1108114.000) diff=2274.583 pctdiff=0.205
SupraTentVolNotVent  1095628.583 (1093354.000) diff=2274.583 pctdiff=0.208
BrainSegVol  1251126.000 (1247891.000) diff=3235.000 pctdiff=0.259
BrainSegVolNotVent  1232173.000 (1232231.583) diff=-58.583 pctdiff=-0.005
BrainSegVolNotVent  1232173.000
CerebellumVol 138605.000
VentChorVol   14760.000
3rd4th5thCSF   4193.000
CSFVol   958.000, OptChiasmVol   214.000
MaskVol 1726540.000
 1158    783   2145  2.296 0.519     0.151     0.036       22     1.7  G&S_frontomargin
 1483    934   2566  2.397 0.554     0.128     0.022       21     1.3  G&S_occipital_inf
 1684    947   2623  2.269 0.553     0.110     0.019       17     1.4  G&S_paracentral
 1934   1272   3555  2.697 0.507     0.141     0.032       30     2.9  G&S_subcentral
 1384    901   3067  2.599 0.517     0.162     0.042       28     2.3  G&S_transv_frontopol
 3376   2313   6853  2.736 0.551     0.126     0.027       45     3.8  G&S_cingul-Ant
 1252    880   2506  2.641 0.448     0.112     0.015        9     0.8  G&S_cingul-Mid-Ant
 1469   1009   2576  2.409 0.424     0.109     0.021       13     1.3  G&S_cingul-Mid-Post
  675    436   1700  3.020 0.424     0.164     0.033       15     1.0  G_cingul-Post-dorsal
  286    176    698  3.027 0.747     0.154     0.040        5     0.4  G_cingul-Post-ventral
 2380   1498   3073  1.832 0.437     0.139     0.031       31     2.9  G_cuneus
 1544    989   4261  3.104 0.504     0.132     0.028       24     1.8  G_front_inf-Opercular
  329    208    983  3.340 0.589     0.158     0.040        7     0.5  G_front_inf-Orbital
 1053    717   2688  2.801 0.448     0.140     0.036       20     1.6  G_front_inf-Triangul
 4902   3183  11852  2.797 0.452     0.145     0.033       84     6.5  G_front_middle
 8141   5190  19107  2.943 0.530     0.121     0.028       92     9.0  G_front_sup
  598    408   1444  3.244 0.505     0.115     0.026        8     0.5  G_Ins_lg&S_cent_ins
  604    399   1963  3.701 0.751     0.100     0.022        5     0.5  G_insular_short
 2812   1723   5853  2.569 0.398     0.135     0.027       46     2.9  G_occipital_middle
 1814   1015   2635  2.149 0.545     0.120     0.024       20     1.8  G_occipital_sup
 2104   1292   4998  2.894 0.506     0.137     0.032       38     2.4  G_oc-temp_lat-fusifor
 3227   2042   4808  2.054 0.708     0.147     0.035       48     4.8  G_oc-temp_med-Lingual
 1653   1072   5197  3.398 0.729     0.125     0.031       22     1.8  G_oc-temp_med-Parahip
 2779   1860   7207  2.850 0.562     0.150     0.037       59     4.2  G_orbital
 4200   2529   9181  2.707 0.552     0.139     0.030       77     5.0  G_pariet_inf-Angular
 2978   1911   6538  2.844 0.457     0.133     0.027       45     3.2  G_pariet_inf-Supramar
 2564   1642   4792  2.272 0.436     0.137     0.028       43     3.0  G_parietal_sup
 2675   1386   3755  2.180 0.545     0.108     0.025       28     2.9  G_postcentral
 3499   1625   6274  2.817 0.463     0.089     0.022       31     3.1  G_precentral
 3019   1990   6256  2.523 0.492     0.151     0.035       58     4.3  G_precuneus
  933    666   2395  2.488 0.608     0.158     0.043       23     1.7  G_rectus
  535    341    875  2.488 1.029     0.104     0.056        8     1.3  G_subcallosal
  637    376   1327  2.726 0.319     0.134     0.024        9     0.5  G_temp_sup-G_T_transv
 2355   1452   6275  3.197 0.549     0.123     0.030       51     2.7  G_temp_sup-Lateral
  976    679   2452  3.400 0.693     0.123     0.032       10     1.4  G_temp_sup-Plan_polar
 1007    641   1978  2.668 0.453     0.101     0.022        9     0.8  G_temp_sup-Plan_tempo
 3322   2117   8645  3.033 0.701     0.140     0.036       59     4.7  G_temporal_inf
 3386   2207   9051  2.994 0.528     0.127     0.027       53     3.7  G_temporal_middle
  401    280    547  2.400 0.381     0.102     0.017        2     0.3  Lat_Fis-ant-Horizont
  380    277    582  2.805 0.287     0.091     0.009        1     0.2  Lat_Fis-ant-Vertical
 1596   1089   2215  2.463 0.393     0.103     0.017        9     1.1  Lat_Fis-post
 3785   2349   4445  1.765 0.452     0.145     0.035       56     5.4  Pole_occipital
 2035   1405   6497  3.258 0.723     0.153     0.045       36     3.7  Pole_temporal
 2058   1433   2554  2.039 0.683     0.125     0.025       21     2.2  S_calcarine
 2958   2037   3377  1.896 0.530     0.101     0.018       16     2.1  S_central
 1518   1040   2102  2.156 0.405     0.111     0.017       11     1.0  S_cingul-Marginalis
  639    440   1074  2.753 0.400     0.115     0.023        4     0.6  S_circular_insula_ant
 1248    856   1857  2.690 0.494     0.089     0.012        5     0.6  S_circular_insula_inf
 1388    957   2077  2.585 0.451     0.111     0.018        8     1.0  S_circular_insula_sup
 1373    968   2251  2.644 0.332     0.085     0.012        5     0.7  S_collat_transv_ant
  389    262    512  2.393 0.407     0.162     0.038        5     0.7  S_collat_transv_post
 2320   1598   3526  2.303 0.392     0.108     0.020       16     1.8  S_front_inf
 2125   1488   2886  2.069 0.383     0.109     0.021       15     1.8  S_front_middle
 2487   1745   3940  2.466 0.389     0.103     0.019       14     1.9  S_front_sup
  449    301    599  2.450 0.400     0.101     0.016        2     0.3  S_interm_prim-Jensen
 4163   2796   5406  2.042 0.441     0.123     0.022       44     3.8  S_intrapariet&P_trans
 1169    797   1405  2.089 0.316     0.110     0.017        7     0.9  S_oc_middle&Lunatus
 1571   1099   1908  2.051 0.398     0.123     0.019       15     1.2  S_oc_sup&transversal
  909    602   1430  2.346 0.455     0.126     0.022       10     0.9  S_occipital_ant
 1366    934   1969  2.590 0.384     0.118     0.021       10     1.2  S_oc-temp_lat
 1990   1413   3000  2.476 0.439     0.115     0.022       15     1.6  S_oc-temp_med&Lingual
  388    279    529  2.159 0.328     0.118     0.015        3     0.3  S_orbital_lateral
  684    499   1041  2.163 0.703     0.113     0.020        6     0.5  S_orbital_med-olfact
 1508   1017   2268  2.208 0.442     0.126     0.029       17     1.8  S_orbital-H_Shaped
 2330   1550   3087  2.201 0.456     0.135     0.027       27     2.6  S_parieto_occipital
 1287    766   1351  2.517 0.831     0.131     0.022       21     0.9  S_pericallosal
 3161   2113   3901  2.098 0.423     0.112     0.020       27     2.5  S_postcentral
 1604   1102   2513  2.557 0.398     0.101     0.016        9     1.1  S_precentral-inf-part
 1814   1229   2548  2.415 0.415     0.105     0.018       11     1.4  S_precentral-sup-part
  411    294    549  2.233 0.515     0.135     0.014        4     0.3  S_suborbital
 1458   1024   2229  2.316 0.482     0.127     0.026       12     1.5  S_subparietal
 2040   1417   2965  2.540 0.493     0.119     0.019       16     1.5  S_temporal_inf
 7170   4918  11507  2.553 0.442     0.111     0.018       59     5.2  S_temporal_sup
  491    343    704  2.522 0.361     0.110     0.012        4     0.2  S_temporal_transverse
#-----------------------------------------
#@# Cortical Parc 3 lh Tue Feb 16 00:15:05 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 stripped lh ../surf/lh.sphere.reg /airflow/apps/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot 

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /airflow/apps/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 1.4   using min determinant for regularization = 0.020
0 singular and 383 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1305 labels changed using aseg
relabeling using gibbs priors...
000:   2158 changed, 148761 examined...
001:    526 changed, 9961 examined...
002:    124 changed, 2955 examined...
003:     51 changed, 779 examined...
004:     24 changed, 283 examined...
005:      9 changed, 143 examined...
006:     11 changed, 61 examined...
007:      8 changed, 65 examined...
008:      6 changed, 47 examined...
009:      7 changed, 35 examined...
010:     11 changed, 38 examined...
011:     10 changed, 52 examined...
012:      4 changed, 53 examined...
013:      3 changed, 22 examined...
014:      2 changed, 17 examined...
015:      2 changed, 14 examined...
016:      3 changed, 14 examined...
017:      2 changed, 17 examined...
018:      0 changed, 14 examined...
218 labels changed using aseg
000: 58 total segments, 25 labels (266 vertices) changed
001: 35 total segments, 2 labels (2 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 8 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
922 vertices marked for relabeling...
922 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 12 seconds.
#-----------------------------------------
#@# Cortical Parc 3 rh Tue Feb 16 00:15:17 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 stripped rh ../surf/rh.sphere.reg /airflow/apps/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot 

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /airflow/apps/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 0.9   using min determinant for regularization = 0.009
0 singular and 325 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1395 labels changed using aseg
relabeling using gibbs priors...
000:   2158 changed, 151498 examined...
001:    515 changed, 9953 examined...
002:    175 changed, 2888 examined...
003:     78 changed, 977 examined...
004:     55 changed, 426 examined...
005:     37 changed, 306 examined...
006:     25 changed, 223 examined...
007:     17 changed, 147 examined...
008:     15 changed, 94 examined...
009:     10 changed, 83 examined...
010:      7 changed, 56 examined...
011:      7 changed, 41 examined...
012:     10 changed, 36 examined...
013:      3 changed, 49 examined...
014:      3 changed, 20 examined...
015:      2 changed, 11 examined...
016:      2 changed, 10 examined...
017:      2 changed, 13 examined...
018:      2 changed, 12 examined...
019:      1 changed, 10 examined...
020:      0 changed, 7 examined...
370 labels changed using aseg
000: 59 total segments, 26 labels (254 vertices) changed
001: 34 total segments, 1 labels (1 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 3 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
631 vertices marked for relabeling...
631 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 12 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 lh Tue Feb 16 00:15:30 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab stripped lh white 

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/wm.mgz...
reading input surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white...
reading input pial surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.pial...
reading input white surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 265930
Total vertex volume 262159 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1687151 mm^3    (det: 1.154671 )
lhCtxGM: 261706.960 261208.000  diff=  499.0  pctdiff= 0.191
rhCtxGM: 265429.723 264692.000  diff=  737.7  pctdiff= 0.278
lhCtxWM: 250863.377 251388.500  diff= -525.1  pctdiff=-0.209
rhCtxWM: 254486.522 254925.500  diff= -439.0  pctdiff=-0.172
SubCortGMVol  61088.000
SupraTentVol  1110388.583 (1108114.000) diff=2274.583 pctdiff=0.205
SupraTentVolNotVent  1095628.583 (1093354.000) diff=2274.583 pctdiff=0.208
BrainSegVol  1251126.000 (1247891.000) diff=3235.000 pctdiff=0.259
BrainSegVolNotVent  1232173.000 (1232231.583) diff=-58.583 pctdiff=-0.005
BrainSegVolNotVent  1232173.000
CerebellumVol 138605.000
VentChorVol   14760.000
3rd4th5thCSF   4193.000
CSFVol   958.000, OptChiasmVol   214.000
MaskVol 1726540.000
 1952   1291   3835  2.784 0.566     0.122     0.020       23     1.5  caudalanteriorcingulate
 3523   2329   6707  2.647 0.453     0.112     0.022       30     3.1  caudalmiddlefrontal
 3123   2036   3944  1.852 0.390     0.136     0.030       39     3.9  cuneus
 1040    750   3898  3.610 0.685     0.137     0.037       15     1.6  entorhinal
 4044   2754   7965  2.680 0.547     0.135     0.029       60     4.4  fusiform
 7808   5243  13756  2.380 0.469     0.128     0.025      101     7.8  inferiorparietal
 4719   3243  11151  2.844 0.604     0.133     0.033       68     6.5  inferiortemporal
 1506    928   2535  2.348 0.806     0.125     0.029       23     1.5  isthmuscingulate
 8257   5172  11781  2.102 0.520     0.142     0.031      115    10.1  lateraloccipital
 4535   3036   9393  2.794 0.618     0.141     0.035       76     6.3  lateralorbitofrontal
 4542   2939   6332  2.100 0.589     0.143     0.034       62     6.4  lingual
 2333   1581   4715  2.551 0.668     0.121     0.030       38     2.5  medialorbitofrontal
 6667   4251  14633  2.857 0.583     0.123     0.030       83     8.7  middletemporal
 1146    749   2646  3.060 0.605     0.125     0.028       12     1.3  parahippocampal
 2608   1665   4452  2.452 0.603     0.110     0.018       20     2.0  paracentral
 2355   1567   5128  2.811 0.476     0.116     0.021       26     2.0  parsopercularis
 1048    673   2368  2.853 0.552     0.117     0.022       13     1.0  parsorbitalis
 2442   1608   4736  2.733 0.442     0.119     0.025       25     2.4  parstriangularis
 1881   1243   1822  1.610 0.407     0.154     0.041       26     3.1  pericalcarine
 7549   4695  10772  2.118 0.591     0.110     0.023       67     7.6  postcentral
 2227   1462   3883  2.495 0.646     0.137     0.030       33     2.6  posteriorcingulate
 7926   4624  13155  2.632 0.570     0.104     0.021       62     6.7  precentral
 6387   4221  10645  2.320 0.479     0.128     0.025       80     6.3  precuneus
 2224   1515   4462  2.854 0.653     0.137     0.032       36     2.8  rostralanteriorcingulate
 6496   4217  12758  2.579 0.491     0.128     0.027       91     6.9  rostralmiddlefrontal
13261   8776  28492  2.820 0.608     0.124     0.027      151    14.0  superiorfrontal
 7123   4600  10890  2.144 0.451     0.115     0.020       79     5.7  superiorparietal
 9930   6629  22150  2.889 0.582     0.119     0.025      122     9.9  superiortemporal
 7910   5232  15035  2.603 0.533     0.124     0.023       95     7.4  supramarginal
 1002    592   1813  2.600 0.425     0.121     0.025       12     1.0  transversetemporal
 2884   1996   6310  3.121 0.768     0.101     0.022       19     2.5  insula
#-----------------------------------------
#@# Parcellation Stats 3 rh Tue Feb 16 00:15:58 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab stripped rh white 

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/wm.mgz...
reading input surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white...
reading input pial surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.pial...
reading input white surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 269042
Total vertex volume 265501 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1687151 mm^3    (det: 1.154671 )
lhCtxGM: 261706.960 261208.000  diff=  499.0  pctdiff= 0.191
rhCtxGM: 265429.723 264692.000  diff=  737.7  pctdiff= 0.278
lhCtxWM: 250863.377 251388.500  diff= -525.1  pctdiff=-0.209
rhCtxWM: 254486.522 254925.500  diff= -439.0  pctdiff=-0.172
SubCortGMVol  61088.000
SupraTentVol  1110388.583 (1108114.000) diff=2274.583 pctdiff=0.205
SupraTentVolNotVent  1095628.583 (1093354.000) diff=2274.583 pctdiff=0.208
BrainSegVol  1251126.000 (1247891.000) diff=3235.000 pctdiff=0.259
BrainSegVolNotVent  1232173.000 (1232231.583) diff=-58.583 pctdiff=-0.005
BrainSegVolNotVent  1232173.000
CerebellumVol 138605.000
VentChorVol   14760.000
3rd4th5thCSF   4193.000
CSFVol   958.000, OptChiasmVol   214.000
MaskVol 1726540.000
  999    648   1838  2.819 0.516     0.133     0.016       15     0.7  caudalanteriorcingulate
 3855   2577   7710  2.671 0.442     0.121     0.025       39     4.0  caudalmiddlefrontal
 3007   1895   3876  1.900 0.424     0.138     0.029       39     3.5  cuneus
  666    458   2270  3.551 0.668     0.114     0.025        5     0.6  entorhinal
 4526   3032   9514  2.794 0.530     0.126     0.026       57     4.5  fusiform
 9898   6425  17513  2.462 0.507     0.128     0.025      132    10.0  inferiorparietal
 6915   4531  14982  2.872 0.647     0.130     0.030       95     8.4  inferiortemporal
 1449    902   2556  2.595 0.670     0.136     0.033       20     1.8  isthmuscingulate
 8226   5156  11876  2.103 0.541     0.133     0.027      106     8.8  lateraloccipital
 4458   3035   8978  2.564 0.609     0.144     0.038       80     7.0  lateralorbitofrontal
 4685   3105   6724  2.058 0.651     0.146     0.034       65     6.7  lingual
 2336   1613   4853  2.435 0.720     0.136     0.038       41     3.8  medialorbitofrontal
 7127   4811  15696  2.793 0.561     0.116     0.021       80     6.2  middletemporal
 1190    765   2536  2.840 0.671     0.116     0.025       12     1.1  parahippocampal
 2645   1718   4534  2.440 0.518     0.106     0.017       19     1.9  paracentral
 2625   1767   5361  2.782 0.496     0.110     0.021       27     2.2  parsopercularis
 1066    700   2579  2.876 0.731     0.137     0.028       16     1.3  parsorbitalis
 2112   1449   4055  2.562 0.523     0.125     0.026       25     2.1  parstriangularis
 2051   1321   2087  1.693 0.467     0.126     0.030       23     2.4  pericalcarine
 8040   4854  11183  2.133 0.603     0.114     0.022       83     7.5  postcentral
 1992   1360   3616  2.475 0.565     0.138     0.025       30     2.1  posteriorcingulate
 8200   4819  13719  2.616 0.546     0.101     0.021       66     7.5  precentral
 6658   4462  11540  2.420 0.517     0.137     0.030       91     7.9  precuneus
 1275    856   2706  2.904 0.636     0.117     0.026       17     1.2  rostralanteriorcingulate
 6504   4350  11792  2.413 0.513     0.131     0.028       82     7.3  rostralmiddlefrontal
15122   9999  31879  2.740 0.565     0.122     0.027      173    16.4  superiorfrontal
 7370   4799  11255  2.139 0.472     0.130     0.025       98     7.4  superiorparietal
 8430   5588  19372  3.007 0.594     0.120     0.026      114     8.4  superiortemporal
 6295   4092  11371  2.638 0.471     0.120     0.024       70     6.1  supramarginal
  724    411   1349  2.692 0.294     0.117     0.020        8     0.5  transversetemporal
 2944   2025   6181  3.003 0.718     0.106     0.019       22     2.3  insula
#-----------------------------------------
#@# WM/GM Contrast lh Tue Feb 16 00:16:27 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 pctsurfcon --s stripped --lh-only 

Log file is /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts/pctsurfcon.log
Tue Feb 16 00:16:28 EST 2021
setenv SUBJECTS_DIR /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
cd /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts
/airflow/apps/freesurfer/bin/pctsurfcon
$Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $
Linux mercury-224.braincode.ca 4.4.0-173-generic #203-Ubuntu SMP Wed Jan 15 02:55:01 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /airflow/apps/freesurfer
mri_vol2surf --mov /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/tmp.pctsurfcon.20574/lh.wm.mgh --regheader stripped --cortex
srcvol = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/orig.mgz as target reference.
-------- original matrix -----------
-0.03979   0.99217   0.11837   0.00004;
-0.99713  -0.04706   0.05932  -0.00001;
 0.06443  -0.11567   0.99120  -0.00002;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/lh.cortex.label
Reading surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 -1 -1 -1
using old
Done mapping volume to surface
Number of source voxels hit = 80322
Masking with /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/lh.cortex.label
Writing to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/tmp.pctsurfcon.20574/lh.wm.mgh
Dim: 148761 1 1
mri_vol2surf --mov /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/tmp.pctsurfcon.20574/lh.gm.mgh --projfrac 0.3 --regheader stripped --cortex
srcvol = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/orig.mgz as target reference.
-------- original matrix -----------
-0.03979   0.99217   0.11837   0.00004;
-0.99713  -0.04706   0.05932  -0.00001;
 0.06443  -0.11567   0.99120  -0.00002;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/lh.cortex.label
Reading surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Done reading source surface
Reading thickness /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
 1 0.3 0.3 0.3
using old
Done mapping volume to surface
Number of source voxels hit = 96847
Masking with /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/lh.cortex.label
Writing to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/tmp.pctsurfcon.20574/lh.gm.mgh
Dim: 148761 1 1
mri_concat /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/tmp.pctsurfcon.20574/lh.wm.mgh /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/tmp.pctsurfcon.20574/lh.gm.mgh --paired-diff-norm --mul 100 --o /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.w-g.pct.mgh
ninputs = 2
Checking inputs
nframestot = 2
Allocing output
Done allocing
Combining pairs
nframes = 1
Multiplying by 100.000000
Writing to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.w-g.pct.mgh
mri_segstats --in /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.w-g.pct.mgh --annot stripped lh aparc --sum /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/stats/lh.w-g.pct.stats --snr

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --in /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.w-g.pct.mgh --annot stripped lh aparc --sum /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname mercury-224.braincode.ca
machine  x86_64
user     airflow
UseRobust  0
Constructing seg from annotation

Reading annotation /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Seg base 1000
Loading /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.w-g.pct.mgh
Vertex Area is 0.652846 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation

Reporting on  35 segmentations
Using PrintSegStat
mri_segstats done
Cleaning up
#-----------------------------------------
#@# WM/GM Contrast rh Tue Feb 16 00:16:34 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts

 pctsurfcon --s stripped --rh-only 

Log file is /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts/pctsurfcon.log
Tue Feb 16 00:16:34 EST 2021
setenv SUBJECTS_DIR /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
cd /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/scripts
/airflow/apps/freesurfer/bin/pctsurfcon
$Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $
Linux mercury-224.braincode.ca 4.4.0-173-generic #203-Ubuntu SMP Wed Jan 15 02:55:01 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /airflow/apps/freesurfer
mri_vol2surf --mov /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/tmp.pctsurfcon.20707/rh.wm.mgh --regheader stripped --cortex
srcvol = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/orig.mgz as target reference.
-------- original matrix -----------
-0.03979   0.99217   0.11837   0.00004;
-0.99713  -0.04706   0.05932  -0.00001;
 0.06443  -0.11567   0.99120  -0.00002;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/rh.cortex.label
Reading surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 -1 -1 -1
using old
Done mapping volume to surface
Number of source voxels hit = 82195
Masking with /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/rh.cortex.label
Writing to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/tmp.pctsurfcon.20707/rh.wm.mgh
Dim: 151498 1 1
mri_vol2surf --mov /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/tmp.pctsurfcon.20707/rh.gm.mgh --projfrac 0.3 --regheader stripped --cortex
srcvol = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/orig.mgz as target reference.
-------- original matrix -----------
-0.03979   0.99217   0.11837   0.00004;
-0.99713  -0.04706   0.05932  -0.00001;
 0.06443  -0.11567   0.99120  -0.00002;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/rh.cortex.label
Reading surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Done reading source surface
Reading thickness /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.thickness
Done
Mapping Source Volume onto Source Subject Surface
 1 0.3 0.3 0.3
using old
Done mapping volume to surface
Number of source voxels hit = 98911
Masking with /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/rh.cortex.label
Writing to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/tmp.pctsurfcon.20707/rh.gm.mgh
Dim: 151498 1 1
mri_concat /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/tmp.pctsurfcon.20707/rh.wm.mgh /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/tmp.pctsurfcon.20707/rh.gm.mgh --paired-diff-norm --mul 100 --o /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.w-g.pct.mgh
ninputs = 2
Checking inputs
nframestot = 2
Allocing output
Done allocing
Combining pairs
nframes = 1
Multiplying by 100.000000
Writing to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.w-g.pct.mgh
mri_segstats --in /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.w-g.pct.mgh --annot stripped rh aparc --sum /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/stats/rh.w-g.pct.stats --snr

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --in /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.w-g.pct.mgh --annot stripped rh aparc --sum /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname mercury-224.braincode.ca
machine  x86_64
user     airflow
UseRobust  0
Constructing seg from annotation

Reading annotation /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Seg base 2000
Loading /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.w-g.pct.mgh
Vertex Area is 0.653332 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation

Reporting on  35 segmentations
Using PrintSegStat
mri_segstats done
Cleaning up
#-----------------------------------------
#@# Relabel Hypointensities Tue Feb 16 00:16:40 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri

 mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz 

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
3213 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
2054 voxels changed to hypointensity...
5235 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Tue Feb 16 00:16:59 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped

 mri_aparc2aseg --s stripped --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /airflow/apps/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt 

relabeling unlikely voxels interior to white matter surface:
	norm: mri/norm.mgz
	 XFORM: mri/transforms/talairach.m3z
	GCA: /airflow/apps/freesurfer/average/RB_all_2016-05-10.vc700.gca
	label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
subject stripped
outvol /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white

Reading lh pial surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.pial

Loading lh annotations from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white

Reading rh pial surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.pial

Loading rh annotations from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.63
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 74
rescaling Left_Lateral_Ventricle from 13 --> 20
rescaling Left_Inf_Lat_Vent from 34 --> 41
rescaling Left_Cerebellum_White_Matter from 86 --> 93
rescaling Left_Cerebellum_Cortex from 60 --> 74
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 98
rescaling Left_Caudate from 75 --> 88
rescaling Left_Putamen from 80 --> 93
rescaling Left_Pallidum from 98 --> 100
rescaling Third_Ventricle from 25 --> 31
rescaling Fourth_Ventricle from 22 --> 21
rescaling Brain_Stem from 81 --> 89
rescaling Left_Hippocampus from 57 --> 72
rescaling Left_Amygdala from 56 --> 74
rescaling CSF from 32 --> 48
rescaling Left_Accumbens_area from 62 --> 71
rescaling Left_VentralDC from 87 --> 97
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 72
rescaling Right_Lateral_Ventricle from 13 --> 20
rescaling Right_Inf_Lat_Vent from 25 --> 29
rescaling Right_Cerebellum_White_Matter from 87 --> 92
rescaling Right_Cerebellum_Cortex from 59 --> 74
rescaling Right_Thalamus_Proper from 85 --> 91
rescaling Right_Caudate from 62 --> 80
rescaling Right_Putamen from 80 --> 86
rescaling Right_Pallidum from 97 --> 100
rescaling Right_Hippocampus from 53 --> 71
rescaling Right_Amygdala from 55 --> 70
rescaling Right_Accumbens_area from 65 --> 78
rescaling Right_VentralDC from 86 --> 99
rescaling Fifth_Ventricle from 40 --> 41
rescaling WM_hypointensities from 78 --> 77
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 525018
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 119 changed.
pass 2: 8 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/aparc+aseg.mgz
#-----------------------------------------
#@# AParc-to-ASeg a2009s Tue Feb 16 00:20:57 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped

 mri_aparc2aseg --s stripped --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /airflow/apps/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s 

relabeling unlikely voxels interior to white matter surface:
	norm: mri/norm.mgz
	 XFORM: mri/transforms/talairach.m3z
	GCA: /airflow/apps/freesurfer/average/RB_all_2016-05-10.vc700.gca
	label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
subject stripped
outvol /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white

Reading lh pial surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.pial

Loading lh annotations from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/lh.aparc.a2009s.annot
reading colortable from annotation file...
colortable with 76 entries read (originally Simple_surface_labels2008.txt)

Reading rh white surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white

Reading rh pial surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.pial

Loading rh annotations from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/rh.aparc.a2009s.annot
reading colortable from annotation file...
colortable with 76 entries read (originally Simple_surface_labels2008.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.63
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 74
rescaling Left_Lateral_Ventricle from 13 --> 20
rescaling Left_Inf_Lat_Vent from 34 --> 41
rescaling Left_Cerebellum_White_Matter from 86 --> 93
rescaling Left_Cerebellum_Cortex from 60 --> 74
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 98
rescaling Left_Caudate from 75 --> 88
rescaling Left_Putamen from 80 --> 93
rescaling Left_Pallidum from 98 --> 100
rescaling Third_Ventricle from 25 --> 31
rescaling Fourth_Ventricle from 22 --> 21
rescaling Brain_Stem from 81 --> 89
rescaling Left_Hippocampus from 57 --> 72
rescaling Left_Amygdala from 56 --> 74
rescaling CSF from 32 --> 48
rescaling Left_Accumbens_area from 62 --> 71
rescaling Left_VentralDC from 87 --> 97
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 72
rescaling Right_Lateral_Ventricle from 13 --> 20
rescaling Right_Inf_Lat_Vent from 25 --> 29
rescaling Right_Cerebellum_White_Matter from 87 --> 92
rescaling Right_Cerebellum_Cortex from 59 --> 74
rescaling Right_Thalamus_Proper from 85 --> 91
rescaling Right_Caudate from 62 --> 80
rescaling Right_Putamen from 80 --> 86
rescaling Right_Pallidum from 97 --> 100
rescaling Right_Hippocampus from 53 --> 71
rescaling Right_Amygdala from 55 --> 70
rescaling Right_Accumbens_area from 65 --> 78
rescaling Right_VentralDC from 86 --> 99
rescaling Fifth_Ventricle from 40 --> 41
rescaling WM_hypointensities from 78 --> 77
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 525057
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 119 changed.
pass 2: 8 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/aparc.a2009s+aseg.mgz
#-----------------------------------------
#@# AParc-to-ASeg DKTatlas Tue Feb 16 00:24:52 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped

 mri_aparc2aseg --s stripped --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /airflow/apps/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz 

relabeling unlikely voxels interior to white matter surface:
	norm: mri/norm.mgz
	 XFORM: mri/transforms/talairach.m3z
	GCA: /airflow/apps/freesurfer/average/RB_all_2016-05-10.vc700.gca
	label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
subject stripped
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white

Reading lh pial surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.pial

Loading lh annotations from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/lh.aparc.DKTatlas.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white

Reading rh pial surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.pial

Loading rh annotations from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/rh.aparc.DKTatlas.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 7.63
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 74
rescaling Left_Lateral_Ventricle from 13 --> 20
rescaling Left_Inf_Lat_Vent from 34 --> 41
rescaling Left_Cerebellum_White_Matter from 86 --> 93
rescaling Left_Cerebellum_Cortex from 60 --> 74
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 98
rescaling Left_Caudate from 75 --> 88
rescaling Left_Putamen from 80 --> 93
rescaling Left_Pallidum from 98 --> 100
rescaling Third_Ventricle from 25 --> 31
rescaling Fourth_Ventricle from 22 --> 21
rescaling Brain_Stem from 81 --> 89
rescaling Left_Hippocampus from 57 --> 72
rescaling Left_Amygdala from 56 --> 74
rescaling CSF from 32 --> 48
rescaling Left_Accumbens_area from 62 --> 71
rescaling Left_VentralDC from 87 --> 97
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 72
rescaling Right_Lateral_Ventricle from 13 --> 20
rescaling Right_Inf_Lat_Vent from 25 --> 29
rescaling Right_Cerebellum_White_Matter from 87 --> 92
rescaling Right_Cerebellum_Cortex from 59 --> 74
rescaling Right_Thalamus_Proper from 85 --> 91
rescaling Right_Caudate from 62 --> 80
rescaling Right_Putamen from 80 --> 86
rescaling Right_Pallidum from 97 --> 100
rescaling Right_Hippocampus from 53 --> 71
rescaling Right_Amygdala from 55 --> 70
rescaling Right_Accumbens_area from 65 --> 78
rescaling Right_VentralDC from 86 --> 99
rescaling Fifth_Ventricle from 40 --> 41
rescaling WM_hypointensities from 78 --> 77
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 525057
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 119 changed.
pass 2: 8 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
#-----------------------------------------
#@# APas-to-ASeg Tue Feb 16 00:28:43 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri

 apas2aseg --i aparc+aseg.mgz --o aseg.mgz 

Tue Feb 16 00:28:45 EST 2021

setenv SUBJECTS_DIR /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
cd /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri
/airflow/apps/freesurfer/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
$Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $
Linux mercury-224.braincode.ca 4.4.0-173-generic #203-Ubuntu SMP Wed Jan 15 02:55:01 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri
cmdline mri_binarize.bin --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 
sysname  Linux
hostname mercury-224.braincode.ca
machine  x86_64
user     airflow

input      aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     aseg.mgz
Binarizing based on threshold
min        -infinity
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Replacing 72
 1:  1000    3
 2:  2000   42
 3:  1001    3
 4:  2001   42
 5:  1002    3
 6:  2002   42
 7:  1003    3
 8:  2003   42
 9:  1004    3
10:  2004   42
11:  1005    3
12:  2005   42
13:  1006    3
14:  2006   42
15:  1007    3
16:  2007   42
17:  1008    3
18:  2008   42
19:  1009    3
20:  2009   42
21:  1010    3
22:  2010   42
23:  1011    3
24:  2011   42
25:  1012    3
26:  2012   42
27:  1013    3
28:  2013   42
29:  1014    3
30:  2014   42
31:  1015    3
32:  2015   42
33:  1016    3
34:  2016   42
35:  1017    3
36:  2017   42
37:  1018    3
38:  2018   42
39:  1019    3
40:  2019   42
41:  1020    3
42:  2020   42
43:  1021    3
44:  2021   42
45:  1022    3
46:  2022   42
47:  1023    3
48:  2023   42
49:  1024    3
50:  2024   42
51:  1025    3
52:  2025   42
53:  1026    3
54:  2026   42
55:  1027    3
56:  2027   42
57:  1028    3
58:  2028   42
59:  1029    3
60:  2029   42
61:  1030    3
62:  2030   42
63:  1031    3
64:  2031   42
65:  1032    3
66:  2032   42
67:  1033    3
68:  2033   42
69:  1034    3
70:  2034   42
71:  1035    3
72:  2035   42
Found 0 values in range
Counting number of voxels in first frame
Found 0 voxels in final mask
Count: 0 0.000000 16777216 0.000000
mri_binarize done
 
Started at Tue Feb 16 00:28:45 EST 2021 
Ended   at Tue Feb 16 00:28:49 EST 2021
Apas2aseg-Run-Time-Sec 4
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Tue Feb 16 00:28:49 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped

 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /airflow/apps/freesurfer/ASegStatsLUT.txt --subject stripped 


$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /airflow/apps/freesurfer/ASegStatsLUT.txt --subject stripped 
sysname  Linux
hostname mercury-224.braincode.ca
machine  x86_64
user     airflow
UseRobust  0
atlas_icv (eTIV) = 1687151 mm^3    (det: 1.154671 )
Computing euler number
orig.nofix lheno =  -40, rheno = -26
orig.nofix lhholes =   21, rhholes = 14
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 261706.960 261208.000  diff=  499.0  pctdiff= 0.191
rhCtxGM: 265429.723 264692.000  diff=  737.7  pctdiff= 0.278
lhCtxWM: 250863.377 251388.500  diff= -525.1  pctdiff=-0.209
rhCtxWM: 254486.522 254925.500  diff= -439.0  pctdiff=-0.172
SubCortGMVol  61088.000
SupraTentVol  1110388.583 (1108114.000) diff=2274.583 pctdiff=0.205
SupraTentVolNotVent  1095628.583 (1093354.000) diff=2274.583 pctdiff=0.208
BrainSegVol  1251126.000 (1247891.000) diff=3235.000 pctdiff=0.259
BrainSegVolNotVent  1232173.000 (1232231.583) diff=-58.583 pctdiff=-0.005
BrainSegVolNotVent  1232173.000
CerebellumVol 138605.000
VentChorVol   14760.000
3rd4th5thCSF   4193.000
CSFVol   958.000, OptChiasmVol   214.000
MaskVol 1726540.000
Loading mri/norm.mgz
Loading mri/norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found  50 segmentations
Computing statistics for each segmentation

Reporting on  45 segmentations
Using PrintSegStat
mri_segstats done
#-----------------------------------------
#@# WMParc Tue Feb 16 00:30:36 EST 2021
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped

 mri_aparc2aseg --s stripped --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz 

SUBJECTS_DIR /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
subject stripped
outvol mri/wmparc.mgz
useribbon 0
baseoffset 0
labeling wm
labeling hypo-intensities as wm
dmaxctx 5.000000
RipUnknown 1
CtxSeg /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/aparc+aseg.mgz

Reading lh white surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white

Reading lh pial surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.pial

Loading lh annotations from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white

Reading rh pial surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.pial

Loading rh annotations from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/ribbon.mgz
Loading filled from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 8353 vertices from left hemi
Ripped 8100 vertices from right hemi

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/aseg.mgz
Loading Ctx Seg File /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/aparc+aseg.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1028513
Used brute-force search on 46 voxels
Fixing Parahip LH WM
  Found 4 clusters
     0 k 1.000000
     1 k 1.000000
     2 k 13.000000
     3 k 1538.000000
Fixing Parahip RH WM
  Found 7 clusters
     0 k 1.000000
     1 k 6.000000
     2 k 3.000000
     3 k 1.000000
     4 k 1534.000000
     5 k 14.000000
     6 k 2.000000
Writing output aseg to mri/wmparc.mgz

 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject stripped --surf-wm-vol --ctab /airflow/apps/freesurfer/WMParcStatsLUT.txt --etiv 


$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject stripped --surf-wm-vol --ctab /airflow/apps/freesurfer/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname mercury-224.braincode.ca
machine  x86_64
user     airflow
UseRobust  0
atlas_icv (eTIV) = 1687151 mm^3    (det: 1.154671 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 261706.960 261208.000  diff=  499.0  pctdiff= 0.191
rhCtxGM: 265429.723 264692.000  diff=  737.7  pctdiff= 0.278
lhCtxWM: 250863.377 251388.500  diff= -525.1  pctdiff=-0.209
rhCtxWM: 254486.522 254925.500  diff= -439.0  pctdiff=-0.172
SubCortGMVol  61088.000
SupraTentVol  1110388.583 (1108114.000) diff=2274.583 pctdiff=0.205
SupraTentVolNotVent  1095628.583 (1093354.000) diff=2274.583 pctdiff=0.208
BrainSegVol  1251126.000 (1247891.000) diff=3235.000 pctdiff=0.259
BrainSegVolNotVent  1232173.000 (1232231.583) diff=-58.583 pctdiff=-0.005
BrainSegVolNotVent  1232173.000
CerebellumVol 138605.000
VentChorVol   14760.000
3rd4th5thCSF   4193.000
CSFVol   958.000, OptChiasmVol   214.000
MaskVol 1726540.000
Loading mri/norm.mgz
Loading mri/norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 390 segmentations
Computing statistics for each segmentation

Reporting on  70 segmentations
Using PrintSegStat
mri_segstats done
/airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label
INFO: fsaverage subject does not exist in SUBJECTS_DIR
INFO: Creating symlink to fsaverage subject...

 cd /airflow/testdata/tutorial_data_20190918_1558/practice_with_data; ln -s /airflow/apps/freesurfer/subjects/fsaverage; cd - 

#--------------------------------------------
#@# BA_exvivo Labels lh Tue Feb 16 00:37:31 EST 2021

 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA1_exvivo.label --trgsubject stripped --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA1_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.BA1_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 4129 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4129 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 476
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4605
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA2_exvivo.label --trgsubject stripped --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA2_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.BA2_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 7909 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  7909 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 789
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 8698
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA3a_exvivo.label --trgsubject stripped --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA3a_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.BA3a_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 4077 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4077 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 189
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4266
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA3b_exvivo.label --trgsubject stripped --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA3b_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.BA3b_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 5983 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  5983 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 680
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6663
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA4a_exvivo.label --trgsubject stripped --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA4a_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.BA4a_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 5784 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  5784 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 526
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6310
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA4p_exvivo.label --trgsubject stripped --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA4p_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.BA4p_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 4070 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4070 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 259
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4329
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA6_exvivo.label --trgsubject stripped --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA6_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.BA6_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 13589 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  13589 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 1942
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 15531
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA44_exvivo.label --trgsubject stripped --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA44_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.BA44_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 4181 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4181 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 366
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4547
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA45_exvivo.label --trgsubject stripped --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA45_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.BA45_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 3422 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3422 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 735
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4157
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.V1_exvivo.label --trgsubject stripped --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.V1_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.V1_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 4641 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4641 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 1329
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 5970
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.V2_exvivo.label --trgsubject stripped --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.V2_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.V2_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 8114 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  8114 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 2665
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 10779
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.MT_exvivo.label --trgsubject stripped --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.MT_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.MT_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 2018 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2018 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 504
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2522
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject stripped --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.entorhinal_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.entorhinal_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 1290 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1290 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 298
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1588
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject stripped --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.perirhinal_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.perirhinal_exvivo.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 1199 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1199 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 243
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1442
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject stripped --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.BA1_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 1014 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1014 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 140
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1154
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject stripped --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.BA2_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 2092 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2092 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 144
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2236
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject stripped --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA3a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.BA3a_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 1504 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1504 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 49
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1553
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject stripped --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA3b_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.BA3b_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 1996 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1996 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 134
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2130
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject stripped --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA4a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.BA4a_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 2319 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2319 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 234
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2553
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject stripped --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA4p_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.BA4p_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 1549 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1549 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 101
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1650
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject stripped --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA6_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.BA6_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 7035 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  7035 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 800
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 7835
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject stripped --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA44_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.BA44_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 1912 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1912 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 131
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2043
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject stripped --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.BA45_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.BA45_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 1151 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1151 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 342
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1493
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject stripped --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.V1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.V1_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 3405 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3405 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 932
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4337
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject stripped --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.V2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.V2_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 3334 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3334 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 1208
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4542
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject stripped --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.MT_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.MT_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 513 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  513 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 138
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 651
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject stripped --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.entorhinal_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.entorhinal_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 470 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  470 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 171
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 641
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject stripped --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/lh.perirhinal_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./lh.perirhinal_exvivo.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 450 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  450 nlabel points
Performing mapping from target back to the source label 148761
Number of reverse mapping hits = 101
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 551
mri_label2label: Done


 mris_label2annot --s stripped --hemi lh --ctab /airflow/apps/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose 

Reading ctab /airflow/apps/freesurfer/average/colortable_BA.txt
Number of ctab entries 15

$Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $
cwd /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label
cmdline mris_label2annot --s stripped --hemi lh --ctab /airflow/apps/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose 
sysname  Linux
hostname mercury-224.braincode.ca
machine  x86_64
user     airflow

subject stripped
hemi    lh
SUBJECTS_DIR /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
ColorTable /airflow/apps/freesurfer/average/colortable_BA.txt
AnnotName  BA_exvivo
nlables 14
LabelThresh 0 0.000000
Loading /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.orig
 1 1530880 BA1_exvivo
 2 16749699 BA2_exvivo
 3 16711680 BA3a_exvivo
 4 3368703 BA3b_exvivo
 5 1376196 BA4a_exvivo
 6 13382655 BA4p_exvivo
 7 10036737 BA6_exvivo
 8 2490521 BA44_exvivo
 9 39283 BA45_exvivo
10 3993 V1_exvivo
11 8508928 V2_exvivo
12 10027163 MT_exvivo
13 16422433 perirhinal_exvivo
14 16392598 entorhinal_exvivo
Mapping unhit to unknown
Found 104659 unhit vertices
Writing annot to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/lh.BA_exvivo.annot

 mris_label2annot --s stripped --hemi lh --ctab /airflow/apps/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose 

Reading ctab /airflow/apps/freesurfer/average/colortable_BA.txt
Number of ctab entries 15

$Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $
cwd /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label
cmdline mris_label2annot --s stripped --hemi lh --ctab /airflow/apps/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose 
sysname  Linux
hostname mercury-224.braincode.ca
machine  x86_64
user     airflow

subject stripped
hemi    lh
SUBJECTS_DIR /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
ColorTable /airflow/apps/freesurfer/average/colortable_BA.txt
AnnotName  BA_exvivo.thresh
nlables 14
LabelThresh 0 0.000000
Loading /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.orig
 1 1530880 BA1_exvivo
 2 16749699 BA2_exvivo
 3 16711680 BA3a_exvivo
 4 3368703 BA3b_exvivo
 5 1376196 BA4a_exvivo
 6 13382655 BA4p_exvivo
 7 10036737 BA6_exvivo
 8 2490521 BA44_exvivo
 9 39283 BA45_exvivo
10 3993 V1_exvivo
11 8508928 V2_exvivo
12 10027163 MT_exvivo
13 16422433 perirhinal_exvivo
14 16392598 entorhinal_exvivo
Mapping unhit to unknown
Found 123342 unhit vertices
Writing annot to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/lh.BA_exvivo.thresh.annot

 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab stripped lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/wm.mgz...
reading input surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white...
reading input pial surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.pial...
reading input white surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 265930
Total vertex volume 262159 (mask=0)
reading colortable from annotation file...
colortable with 15 entries read (originally /airflow/apps/freesurfer/average/colortable_BA.txt)
Saving annotation colortable ./BA_exvivo.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1687151 mm^3    (det: 1.154671 )
lhCtxGM: 261706.960 261208.000  diff=  499.0  pctdiff= 0.191
rhCtxGM: 265429.723 264692.000  diff=  737.7  pctdiff= 0.278
lhCtxWM: 250863.377 251388.500  diff= -525.1  pctdiff=-0.209
rhCtxWM: 254486.522 254925.500  diff= -439.0  pctdiff=-0.172
SubCortGMVol  61088.000
SupraTentVol  1110388.583 (1108114.000) diff=2274.583 pctdiff=0.205
SupraTentVolNotVent  1095628.583 (1093354.000) diff=2274.583 pctdiff=0.208
BrainSegVol  1251126.000 (1247891.000) diff=3235.000 pctdiff=0.259
BrainSegVolNotVent  1232173.000 (1232231.583) diff=-58.583 pctdiff=-0.005
BrainSegVolNotVent  1232173.000
CerebellumVol 138605.000
VentChorVol   14760.000
3rd4th5thCSF   4193.000
CSFVol   958.000, OptChiasmVol   214.000
MaskVol 1726540.000
 1300    660   1857  2.196 0.494     0.122     0.029       17     1.6  BA1_exvivo
 4157   2676   6011  2.189 0.495     0.105     0.019       35     3.2  BA2_exvivo
 1098    768   1046  1.779 0.387     0.149     0.028       12     1.2  BA3a_exvivo
 2674   1668   4031  2.066 0.718     0.105     0.024       24     3.0  BA3b_exvivo
 1773    956   2899  2.684 0.477     0.086     0.018       10     1.3  BA4a_exvivo
 1295    825   1934  2.407 0.484     0.087     0.016        6     0.8  BA4p_exvivo
10847   6606  22261  2.854 0.549     0.107     0.023       93     9.8  BA6_exvivo
 2144   1440   4901  2.941 0.521     0.114     0.020       21     1.6  BA44_exvivo
 3180   2079   6654  2.747 0.457     0.124     0.027       39     3.3  BA45_exvivo
 3472   2203   3697  1.690 0.469     0.145     0.037       48     5.1  V1_exvivo
 8312   5244  10351  1.895 0.471     0.149     0.035      120    12.1  V2_exvivo
 2195   1456   3568  2.411 0.454     0.139     0.030       29     2.4  MT_exvivo
  845    580   2785  3.536 0.547     0.132     0.031       11     1.2  perirhinal_exvivo
  810    604   2635  3.177 0.697     0.146     0.040       14     1.1  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab stripped lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/wm.mgz...
reading input surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white...
reading input pial surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.pial...
reading input white surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 265930
Total vertex volume 262159 (mask=0)
reading colortable from annotation file...
colortable with 15 entries read (originally /airflow/apps/freesurfer/average/colortable_BA.txt)
Saving annotation colortable ./BA_exvivo.thresh.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1687151 mm^3    (det: 1.154671 )
lhCtxGM: 261706.960 261208.000  diff=  499.0  pctdiff= 0.191
rhCtxGM: 265429.723 264692.000  diff=  737.7  pctdiff= 0.278
lhCtxWM: 250863.377 251388.500  diff= -525.1  pctdiff=-0.209
rhCtxWM: 254486.522 254925.500  diff= -439.0  pctdiff=-0.172
SubCortGMVol  61088.000
SupraTentVol  1110388.583 (1108114.000) diff=2274.583 pctdiff=0.205
SupraTentVolNotVent  1095628.583 (1093354.000) diff=2274.583 pctdiff=0.208
BrainSegVol  1251126.000 (1247891.000) diff=3235.000 pctdiff=0.259
BrainSegVolNotVent  1232173.000 (1232231.583) diff=-58.583 pctdiff=-0.005
BrainSegVolNotVent  1232173.000
CerebellumVol 138605.000
VentChorVol   14760.000
3rd4th5thCSF   4193.000
CSFVol   958.000, OptChiasmVol   214.000
MaskVol 1726540.000
  840    405   1074  2.069 0.425     0.127     0.032       12     1.1  BA1_exvivo
 1513   1002   2100  1.971 0.430     0.085     0.013        8     0.9  BA2_exvivo
  847    599    794  1.755 0.375     0.154     0.029       10     0.9  BA3a_exvivo
 1450    936   1613  1.671 0.454     0.086     0.015        7     1.0  BA3b_exvivo
 1748    946   2796  2.629 0.520     0.084     0.016        9     1.4  BA4a_exvivo
 1105    699   1531  2.304 0.476     0.093     0.017        6     0.8  BA4p_exvivo
 5844   3414  10979  2.817 0.502     0.103     0.023       44     5.1  BA6_exvivo
 1389    929   3035  2.880 0.513     0.104     0.016       12     0.8  BA44_exvivo
 1351    852   3165  2.912 0.448     0.128     0.030       19     1.7  BA45_exvivo
 3702   2335   3911  1.674 0.461     0.140     0.035       48     5.2  V1_exvivo
 4138   2597   4470  1.746 0.392     0.159     0.041       67     7.1  V2_exvivo
  584    378    967  2.505 0.433     0.148     0.027        9     0.6  MT_exvivo
  446    316   1426  3.551 0.487     0.130     0.030        6     0.6  perirhinal_exvivo
  462    330   1717  3.249 0.639     0.162     0.052       11     0.9  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Tue Feb 16 00:42:04 EST 2021

 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA1_exvivo.label --trgsubject stripped --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA1_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.BA1_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 3962 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3962 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 506
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4468
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA2_exvivo.label --trgsubject stripped --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA2_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.BA2_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 6687 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  6687 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 687
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7374
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA3a_exvivo.label --trgsubject stripped --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA3a_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.BA3a_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 3980 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3980 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 98
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4078
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA3b_exvivo.label --trgsubject stripped --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA3b_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.BA3b_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 4522 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4522 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 280
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 4802
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA4a_exvivo.label --trgsubject stripped --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA4a_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.BA4a_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 5747 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  5747 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 553
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6300
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA4p_exvivo.label --trgsubject stripped --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA4p_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.BA4p_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 4473 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4473 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 241
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4714
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA6_exvivo.label --trgsubject stripped --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA6_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.BA6_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 12256 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  12256 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 1600
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 13856
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA44_exvivo.label --trgsubject stripped --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA44_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.BA44_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 6912 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  6912 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 961
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 7873
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA45_exvivo.label --trgsubject stripped --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA45_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.BA45_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 5355 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  5355 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 956
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 6311
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.V1_exvivo.label --trgsubject stripped --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.V1_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.V1_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 4727 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  4727 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 1378
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 6105
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.V2_exvivo.label --trgsubject stripped --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.V2_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.V2_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 8016 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  8016 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 3026
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 11042
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.MT_exvivo.label --trgsubject stripped --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.MT_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.MT_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 1932 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1932 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 685
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2617
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject stripped --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.entorhinal_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.entorhinal_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 1038 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1038 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 213
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1251
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject stripped --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.perirhinal_exvivo.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.perirhinal_exvivo.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 752 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  752 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 184
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 936
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject stripped --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.BA1_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 876 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  876 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 149
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1025
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject stripped --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.BA2_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 2688 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2688 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 260
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2948
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject stripped --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA3a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.BA3a_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 1698 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1698 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 32
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1730
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject stripped --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA3b_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.BA3b_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 2183 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  2183 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 86
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2269
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject stripped --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA4a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.BA4a_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 1388 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1388 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 65
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1453
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject stripped --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA4p_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.BA4p_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 1489 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1489 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 67
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1556
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject stripped --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA6_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.BA6_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 6959 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  6959 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 932
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 7891
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject stripped --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA44_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.BA44_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 1012 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1012 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 160
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1172
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject stripped --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.BA45_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.BA45_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 1178 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  1178 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 225
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1403
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject stripped --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.V1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.V1_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 3232 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3232 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 880
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4112
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject stripped --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.V2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.V2_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 3437 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  3437 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 1322
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 4759
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject stripped --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.MT_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.MT_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 268 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  268 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 105
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 373
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject stripped --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.entorhinal_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.entorhinal_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 694 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  694 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 154
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 848
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject stripped --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 


srclabel = /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/label/rh.perirhinal_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = stripped
trglabel = ./rh.perirhinal_exvivo.thresh.label
regmethod = surface

srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
FREESURFER_HOME /airflow/apps/freesurfer
Loading source label.
Found 291 points in source label.
Starting surface-based mapping
Reading source registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white
Reading target registration 
 /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found  291 nlabel points
Performing mapping from target back to the source label 151498
Number of reverse mapping hits = 97
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 388
mri_label2label: Done


 mris_label2annot --s stripped --hemi rh --ctab /airflow/apps/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose 

Reading ctab /airflow/apps/freesurfer/average/colortable_BA.txt
Number of ctab entries 15

$Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $
cwd /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label
cmdline mris_label2annot --s stripped --hemi rh --ctab /airflow/apps/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose 
sysname  Linux
hostname mercury-224.braincode.ca
machine  x86_64
user     airflow

subject stripped
hemi    rh
SUBJECTS_DIR /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
ColorTable /airflow/apps/freesurfer/average/colortable_BA.txt
AnnotName  BA_exvivo
nlables 14
LabelThresh 0 0.000000
Loading /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.orig
 1 1530880 BA1_exvivo
 2 16749699 BA2_exvivo
 3 16711680 BA3a_exvivo
 4 3368703 BA3b_exvivo
 5 1376196 BA4a_exvivo
 6 13382655 BA4p_exvivo
 7 10036737 BA6_exvivo
 8 2490521 BA44_exvivo
 9 39283 BA45_exvivo
10 3993 V1_exvivo
11 8508928 V2_exvivo
12 10027163 MT_exvivo
13 16422433 perirhinal_exvivo
14 16392598 entorhinal_exvivo
Mapping unhit to unknown
Found 106604 unhit vertices
Writing annot to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/rh.BA_exvivo.annot

 mris_label2annot --s stripped --hemi rh --ctab /airflow/apps/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose 

Reading ctab /airflow/apps/freesurfer/average/colortable_BA.txt
Number of ctab entries 15

$Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $
cwd /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label
cmdline mris_label2annot --s stripped --hemi rh --ctab /airflow/apps/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose 
sysname  Linux
hostname mercury-224.braincode.ca
machine  x86_64
user     airflow

subject stripped
hemi    rh
SUBJECTS_DIR /airflow/testdata/tutorial_data_20190918_1558/practice_with_data
ColorTable /airflow/apps/freesurfer/average/colortable_BA.txt
AnnotName  BA_exvivo.thresh
nlables 14
LabelThresh 0 0.000000
Loading /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.orig
 1 1530880 BA1_exvivo
 2 16749699 BA2_exvivo
 3 16711680 BA3a_exvivo
 4 3368703 BA3b_exvivo
 5 1376196 BA4a_exvivo
 6 13382655 BA4p_exvivo
 7 10036737 BA6_exvivo
 8 2490521 BA44_exvivo
 9 39283 BA45_exvivo
10 3993 V1_exvivo
11 8508928 V2_exvivo
12 10027163 MT_exvivo
13 16422433 perirhinal_exvivo
14 16392598 entorhinal_exvivo
Mapping unhit to unknown
Found 126597 unhit vertices
Writing annot to /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/label/rh.BA_exvivo.thresh.annot

 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab stripped rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/wm.mgz...
reading input surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white...
reading input pial surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.pial...
reading input white surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 269042
Total vertex volume 265501 (mask=0)
reading colortable from annotation file...
colortable with 15 entries read (originally /airflow/apps/freesurfer/average/colortable_BA.txt)
Saving annotation colortable ./BA_exvivo.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1687151 mm^3    (det: 1.154671 )
lhCtxGM: 261706.960 261208.000  diff=  499.0  pctdiff= 0.191
rhCtxGM: 265429.723 264692.000  diff=  737.7  pctdiff= 0.278
lhCtxWM: 250863.377 251388.500  diff= -525.1  pctdiff=-0.209
rhCtxWM: 254486.522 254925.500  diff= -439.0  pctdiff=-0.172
SubCortGMVol  61088.000
SupraTentVol  1110388.583 (1108114.000) diff=2274.583 pctdiff=0.205
SupraTentVolNotVent  1095628.583 (1093354.000) diff=2274.583 pctdiff=0.208
BrainSegVol  1251126.000 (1247891.000) diff=3235.000 pctdiff=0.259
BrainSegVolNotVent  1232173.000 (1232231.583) diff=-58.583 pctdiff=-0.005
BrainSegVolNotVent  1232173.000
CerebellumVol 138605.000
VentChorVol   14760.000
3rd4th5thCSF   4193.000
CSFVol   958.000, OptChiasmVol   214.000
MaskVol 1726540.000
 1192    546   1586  2.223 0.518     0.120     0.031       15     1.5  BA1_exvivo
 3977   2521   5377  2.172 0.475     0.105     0.020       32     3.2  BA2_exvivo
 1032    714   1001  1.754 0.372     0.141     0.029       11     1.0  BA3a_exvivo
 2055   1302   2553  1.773 0.564     0.100     0.016       15     1.7  BA3b_exvivo
 1725    976   2976  2.659 0.475     0.079     0.014        8     1.1  BA4a_exvivo
 1269    817   1942  2.396 0.441     0.092     0.017        7     0.8  BA4p_exvivo
 9444   5653  17931  2.766 0.505     0.102     0.021       75     8.1  BA6_exvivo
 4000   2682   8037  2.738 0.538     0.113     0.023       41     4.1  BA44_exvivo
 4255   2886   8546  2.629 0.582     0.129     0.026       56     4.7  BA45_exvivo
 3757   2434   4311  1.698 0.484     0.129     0.030       43     4.7  V1_exvivo
 8523   5384  10990  1.953 0.540     0.143     0.032      118    11.3  V2_exvivo
 2435   1603   3916  2.381 0.409     0.124     0.023       27     2.2  MT_exvivo
  728    495   2199  3.389 0.713     0.117     0.029        8     0.7  perirhinal_exvivo
  502    336   1837  3.465 0.674     0.159     0.048       11     1.0  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab stripped rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/mri/wm.mgz...
reading input surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white...
reading input pial surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.pial...
reading input white surface /airflow/testdata/tutorial_data_20190918_1558/practice_with_data/stripped/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 269042
Total vertex volume 265501 (mask=0)
reading colortable from annotation file...
colortable with 15 entries read (originally /airflow/apps/freesurfer/average/colortable_BA.txt)
Saving annotation colortable ./BA_exvivo.thresh.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1687151 mm^3    (det: 1.154671 )
lhCtxGM: 261706.960 261208.000  diff=  499.0  pctdiff= 0.191
rhCtxGM: 265429.723 264692.000  diff=  737.7  pctdiff= 0.278
lhCtxWM: 250863.377 251388.500  diff= -525.1  pctdiff=-0.209
rhCtxWM: 254486.522 254925.500  diff= -439.0  pctdiff=-0.172
SubCortGMVol  61088.000
SupraTentVol  1110388.583 (1108114.000) diff=2274.583 pctdiff=0.205
SupraTentVolNotVent  1095628.583 (1093354.000) diff=2274.583 pctdiff=0.208
BrainSegVol  1251126.000 (1247891.000) diff=3235.000 pctdiff=0.259
BrainSegVolNotVent  1232173.000 (1232231.583) diff=-58.583 pctdiff=-0.005
BrainSegVolNotVent  1232173.000
CerebellumVol 138605.000
VentChorVol   14760.000
3rd4th5thCSF   4193.000
CSFVol   958.000, OptChiasmVol   214.000
MaskVol 1726540.000
  829    363   1007  2.142 0.467     0.119     0.032       11     1.2  BA1_exvivo
 2255   1377   3156  2.160 0.449     0.100     0.017       18     1.6  BA2_exvivo
  938    652    819  1.717 0.303     0.142     0.028        9     1.0  BA3a_exvivo
 1517   1000   1656  1.594 0.404     0.090     0.014        9     1.0  BA3b_exvivo
  969    567   1759  2.705 0.457     0.081     0.016        5     0.7  BA4a_exvivo
 1016    679   1629  2.454 0.460     0.084     0.016        4     0.6  BA4p_exvivo
 6153   3548  11264  2.738 0.484     0.101     0.022       49     5.4  BA6_exvivo
  993    693   2642  3.118 0.512     0.116     0.024       11     0.9  BA44_exvivo
 1188    822   2810  2.859 0.392     0.131     0.030       20     1.5  BA45_exvivo
 3563   2308   3995  1.694 0.486     0.127     0.030       40     4.4  V1_exvivo
 4336   2767   5367  1.808 0.550     0.153     0.037       68     6.4  V2_exvivo
  346    205    634  2.554 0.360     0.138     0.038        5     0.5  MT_exvivo
  442    301   1192  3.335 0.698     0.106     0.024        3     0.3  perirhinal_exvivo
  356    229   1281  3.613 0.564     0.151     0.043        8     0.6  entorhinal_exvivo

Started at Mon Feb 15 16:52:17 EST 2021 
Ended   at Tue Feb 16 00:46:47 EST 2021
#@#%# recon-all-run-time-hours 7.908
recon-all -s stripped finished without error at Tue Feb 16 00:46:47 EST 2021



#New# invocation of recon-all 




Thu Feb 18 16:02:29 UTC 2021
cd /data/skullstrip1_before
setenv SUBJECTS_DIR /data
/usr/local/freesurfer/bin/recon-all -skullstrip -wsthresh 1 -clean-bm -no-wsgcaatlas -subjid skullstrip1_before

subjid skullstrip1_before
setenv SUBJECTS_DIR /data
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
Linux d577c4268a40 4.15.0-123-generic #126-Ubuntu SMP Wed Oct 21 09:40:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize unlimited
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1048576 
memorylocked 16384 kbytes
maxproc      unlimited
maxlocks     unlimited
maxsignal    63130 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:            15G        1.6G        1.7G         33M         12G         13G
Swap:          4.1G        237M        3.9G

########################################
program versions used
7.1.1 (freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551)
7.1.1

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:29-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:29-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:30-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:30-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:30-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:30-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:33-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:33-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:33-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:33-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:33-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:33-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:33-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:33-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:33-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:34-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:34-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:34-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.1

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:34-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.1

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:35-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:35-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:35-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:35-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:35-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:36-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:36-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:36-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:36-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:36-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:36-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:36-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:36-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:36-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:37-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:37-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:37-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:37-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:37-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:37-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:37-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:37-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:37-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:37-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.1
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:02:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: d577c4268a40  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /usr/local/freesurfer/average
GCA RB_all_2020-01-02.gca
GCASkull RB_all_withskull_2020_01_02.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /usr/local/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################

 mv -f /data/skullstrip1_before/mri/brainmask.mgz /data/skullstrip1_before/trash 

#--------------------------------------------
#@# Skull Stripping Thu Feb 18 16:02:39 UTC 2021
/data/skullstrip1_before/mri

 mri_watershed -T1 -h 1 T1.mgz brainmask.auto.mgz 


Mode:          T1 normalized volume
Mode:          Preflooding height manually specified
--------------------------------------------------------------------------
ERROR: FreeSurfer license file /usr/local/freesurfer/.license not found.
  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu/registration.html to 
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.
  A path to an alternative license file can also be
  specified with the FS_LICENSE environmental variable.
--------------------------------------------------------------------------

*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
Linux d577c4268a40 4.15.0-123-generic #126-Ubuntu SMP Wed Oct 21 09:40:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s skullstrip1_before exited with ERRORS at Thu Feb 18 16:02:39 UTC 2021

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



#New# invocation of recon-all 




Thu Feb 18 16:05:54 UTC 2021
cd /data/skullstrip1_before
setenv SUBJECTS_DIR /data
/usr/local/freesurfer/bin/recon-all -skullstrip -wsthresh 1 -clean-bm -no-wsgcaatlas -subjid skullstrip1_before

subjid skullstrip1_before
setenv SUBJECTS_DIR /data
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
Linux eb6e7cc777ac 4.15.0-123-generic #126-Ubuntu SMP Wed Oct 21 09:40:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize unlimited
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1048576 
memorylocked 16384 kbytes
maxproc      unlimited
maxlocks     unlimited
maxsignal    63130 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:            15G        1.6G        1.5G         33M         12G         13G
Swap:          4.1G        237M        3.9G

########################################
program versions used
7.1.1 (freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551)
7.1.1

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:54-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:54-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:54-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:54-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:54-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.1

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.1

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.1
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/18-16:05:55-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: root  Machine: eb6e7cc777ac  Platform: Linux  PlatformVersion: 4.15.0-123-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /usr/local/freesurfer/average
GCA RB_all_2020-01-02.gca
GCASkull RB_all_withskull_2020_01_02.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /usr/local/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################

 mv -f /data/skullstrip1_before/mri/brainmask.mgz /data/skullstrip1_before/trash 

mv: cannot stat '/data/skullstrip1_before/mri/brainmask.mgz': No such file or directory
#--------------------------------------------
#@# Skull Stripping Thu Feb 18 16:05:56 UTC 2021
/data/skullstrip1_before/mri

 mri_watershed -T1 -h 1 T1.mgz brainmask.auto.mgz 


Mode:          T1 normalized volume
Mode:          Preflooding height manually specified

*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz

*************************WATERSHED**************************
Sorting...
      T1-weighted MRI image
      Count how many 110 voxels are present :  350210

      Find the largest 110-component...
             heap usage = 250864 Kbytes.
             current max segment has 173585 voxels
             removing small segments (less than 1 percent of maxarea).
             heap usage = 165232 Kbytes.
             removing small segments (less than 1 percent of maxarea).done
      And identify it as the main brain basin...done
      Main component: 173585 voxels
      first estimation of the COG coord: x=126 y=115 z=112 r=89
      first estimation of the main basin volume: 2981949 voxels
      global maximum in x=149, y=94, z=69, Imax=255
      CSF=17, WM_intensity=110, WM_VARIANCE=5
      WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
      preflooding height equal to 1 percent
done.
Analyze...

      main basin size=  989740 voxels, voxel volume =1.000 
                     = 989740 mmm3 = 989.740 cm3
done.
PostAnalyze...
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 194 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 47 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2545 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 29 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2714 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 15 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 231 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 13 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 141 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 298 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 86 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 17 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 62 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 26 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 17 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 7 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 219 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 15 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 23 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 18 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 15 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 20 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 45 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 27 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 20 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 18 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 10 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 52 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 226 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 42 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 965 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 76 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 184 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 19 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 42 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 23 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 26 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 29 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 10 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 173 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 41 voxels
      ambiguous basin, merged: at least 17 ambiguous voxels; size: 4729 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1136 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 554 voxels
      ambiguous basin, merged: at least 15 ambiguous voxels; size: 3366 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 10 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 29 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 153 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1419 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
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      ambiguous basin, merged: at least 3 ambiguous voxels; size: 27 voxels
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      ambiguous basin, merged: at least 13 ambiguous voxels; size: 1804 voxels
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      ambiguous basin, merged: at least 13 ambiguous voxels; size: 1872 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1450 voxels
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      ambiguous basin, merged: at least 9 ambiguous voxels; size: 577 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 130 voxels
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      ambiguous basin, merged: at least 10 ambiguous voxels; size: 833 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 507 voxels
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      ambiguous basin, merged: at least 6 ambiguous voxels; size: 172 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 204 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
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      ambiguous basin, merged: at least 3 ambiguous voxels; size: 20 voxels
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      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
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      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1170 voxels
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      ambiguous basin, merged: at least 10 ambiguous voxels; size: 901 voxels
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      ambiguous basin, merged: at least 3 ambiguous voxels; size: 25 voxels
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      ambiguous basin, merged: at least 10 ambiguous voxels; size: 833 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 633 voxels
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      ambiguous basin, merged: at least 3 ambiguous voxels; size: 18 voxels
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      ambiguous basin, merged: at least 7 ambiguous voxels; size: 310 voxels
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      ambiguous basin, merged: at least 8 ambiguous voxels; size: 462 voxels
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      ambiguous basin, merged: at least 3 ambiguous voxels; size: 17 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 8 voxels
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      ambiguous basin, merged: at least 4 ambiguous voxels; size: 33 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 42 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 71 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1283 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 108 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 91 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 41 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 633 voxels
      ambiguous basin, merged: at least 13 ambiguous voxels; size: 2012 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 488 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 69 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 996 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 56 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 20 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 255 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 81 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 703 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 25 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 922 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 33 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 47 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 89 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 23 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1126 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 913 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 266 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 868 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 642 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 444 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 13 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 278 voxels
      ***** 264 basin(s) merged in 7 iteration(s)
      ***** 128123 voxel(s) added to the main basin
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 12 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 8 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 13 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 20 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 36 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 11 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 162 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 16 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 6 ambiguous voxels; size: 599 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 8 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 25 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 11 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 53 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 64 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 10 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 26 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 18 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 35 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 41 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 11 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 16 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 26 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 8 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 8 voxels
      ambiguous basin, non merged: 5 ambiguous voxels; size: 132 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 14 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 11 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 43 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 13 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 216 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 57 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
done.

****************TEMPLATE DEFORMATION****************

      second estimation of the COG coord: x=125,y=94, z=117, r=9469 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=25, CSF_MAX=63 , nb = 22554
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    63,      60,        59,   78
  after  analyzing :    51,      60,        60,   64
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...67 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.013
curvature mean = 63.906, std = 8.683

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 4.33, sigma = 6.39
      after  rotation: sse = 4.33, sigma = 6.39
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  5.11, its var is  7.79   
      before Erosion-Dilatation  2.59% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...39 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1388799 voxels, voxel volume = 1.000 mm3
           = 1388799 mmm3 = 1388.799 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    17.632210
mri_watershed stimesec    0.378875
mri_watershed ru_maxrss   348964
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   163297
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  16624
mri_watershed ru_oublock  2120
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    82
mri_watershed ru_nivcsw   1497
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#@# white curv lh Thu Feb 18 16:06:16 UTC 2021
cd /data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
   Update not needed
#@# white area lh Thu Feb 18 16:06:16 UTC 2021
cd /data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
   Update not needed
#@# pial curv lh Thu Feb 18 16:06:17 UTC 2021
cd /data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
   Update not needed
#@# pial area lh Thu Feb 18 16:06:17 UTC 2021
cd /data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
   Update not needed
#@# thickness lh Thu Feb 18 16:06:18 UTC 2021
cd /data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness
   Update not needed
#@# area and vertex vol lh Thu Feb 18 16:06:18 UTC 2021
cd /data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness
   Update not needed
#@# white curv rh Thu Feb 18 16:06:19 UTC 2021
cd /data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
   Update not needed
#@# white area rh Thu Feb 18 16:06:19 UTC 2021
cd /data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
   Update not needed
#@# pial curv rh Thu Feb 18 16:06:20 UTC 2021
cd /data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
   Update not needed
#@# pial area rh Thu Feb 18 16:06:20 UTC 2021
cd /data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
   Update not needed
#@# thickness rh Thu Feb 18 16:06:21 UTC 2021
cd /data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness
   Update not needed
#@# area and vertex vol rh Thu Feb 18 16:06:21 UTC 2021
cd /data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness
   Update not needed

Started at Thu Feb 18 16:05:54 UTC 2021 
Ended   at Thu Feb 18 16:06:21 UTC 2021
#@#%# recon-all-run-time-hours 0.007
recon-all -s skullstrip1_before finished without error at Thu Feb 18 16:06:21 UTC 2021



#New# invocation of recon-all 




Fri Feb 19 19:10:45 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before
setenv SUBJECTS_DIR /mnt/vredemo/practice_with_data
/mnt/vredemo/freesurfer/bin/recon-all -skullstrip -wsthresh 1 -clean-bm -no-wsgcaatlas -subjid skullstrip1_before

subjid skullstrip1_before
setenv SUBJECTS_DIR /mnt/vredemo/practice_with_data
FREESURFER_HOME /mnt/vredemo/freesurfer
Actual FREESURFER_HOME /mnt/vredemo/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
Linux ivysaur-12.ldap.indocresearch.org 5.4.0-53-generic #59-Ubuntu SMP Wed Oct 21 09:38:44 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 65536 kbytes
maxproc      63380 
maxlocks     unlimited
maxsignal    63380 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           15Gi       3.4Gi       5.5Gi        63Mi       6.7Gi        11Gi
Swap:            0B          0B          0B

########################################
program versions used
7.1.1 (freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551)
7.1.1

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:45-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:45-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:46-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:46-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:46-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:46-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:46-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:46-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:46-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:46-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:46-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:46-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:46-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:46-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:47-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:47-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:47-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:47-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:47-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:47-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:47-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:47-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:47-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:47-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:47-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:47-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:47-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:47-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:47-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:47-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:48-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:48-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:48-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:48-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.1

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:48-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.1

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:48-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:48-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:48-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:48-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:48-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:48-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:48-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:49-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:49-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:49-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:49-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:49-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:49-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:49-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:49-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:49-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:49-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:49-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:49-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:50-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:50-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:50-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:50-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:50-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:50-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:50-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:50-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:50-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:50-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:50-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:50-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:50-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:50-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:50-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:50-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:51-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:51-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.1
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:10:51-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /mnt/vredemo/freesurfer/average
GCA RB_all_2020-01-02.gca
GCASkull RB_all_withskull_2020_01_02.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /mnt/vredemo/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################

 mv -f /mnt/vredemo/practice_with_data/skullstrip1_before/mri/brainmask.mgz /mnt/vredemo/practice_with_data/skullstrip1_before/trash 

#--------------------------------------------
#@# Skull Stripping Fri Feb 19 19:10:51 UTC 2021
/mnt/vredemo/practice_with_data/skullstrip1_before/mri

 mri_watershed -T1 -h 1 T1.mgz brainmask.auto.mgz 


Mode:          T1 normalized volume
Mode:          Preflooding height manually specified
--------------------------------------------------------------------------
ERROR: FreeSurfer license file /mnt/vredemo/freesurfer/.license not found.
  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu/registration.html to 
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.
  A path to an alternative license file can also be
  specified with the FS_LICENSE environmental variable.
--------------------------------------------------------------------------

*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
Command exited with non-zero status 255
@#@FSTIME  2021:02:19:19:10:51 mri_watershed N 5 e 0.01 S 0.00 U 0.00 P 33% M 6260 F 1 R 252 W 0 c 5 w 21 I 512 O 0 L 0.30 0.27 0.18
@#@FSLOADPOST 2021:02:19:19:10:51 mri_watershed N 5 0.30 0.27 0.18
Linux ivysaur-12.ldap.indocresearch.org 5.4.0-53-generic #59-Ubuntu SMP Wed Oct 21 09:38:44 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s skullstrip1_before exited with ERRORS at Fri Feb 19 19:10:51 UTC 2021

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



#New# invocation of recon-all 




Fri Feb 19 19:11:38 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before
setenv SUBJECTS_DIR /mnt/vredemo/practice_with_data
/mnt/vredemo/freesurfer/bin/recon-all -skullstrip -wsthresh 1 -clean-bm -no-wsgcaatlas -subjid skullstrip1_before

subjid skullstrip1_before
setenv SUBJECTS_DIR /mnt/vredemo/practice_with_data
FREESURFER_HOME /mnt/vredemo/freesurfer
Actual FREESURFER_HOME /mnt/vredemo/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
Linux ivysaur-12.ldap.indocresearch.org 5.4.0-53-generic #59-Ubuntu SMP Wed Oct 21 09:38:44 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 65536 kbytes
maxproc      63380 
maxlocks     unlimited
maxsignal    63380 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           15Gi       3.3Gi       5.5Gi        63Mi       6.7Gi        11Gi
Swap:            0B          0B          0B

########################################
program versions used
7.1.1 (freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551)
7.1.1

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.1

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.1

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:38-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.1
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-19:11:39-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /mnt/vredemo/freesurfer/average
GCA RB_all_2020-01-02.gca
GCASkull RB_all_withskull_2020_01_02.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /mnt/vredemo/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################

 mv -f /mnt/vredemo/practice_with_data/skullstrip1_before/mri/brainmask.mgz /mnt/vredemo/practice_with_data/skullstrip1_before/trash 

mv: cannot stat '/mnt/vredemo/practice_with_data/skullstrip1_before/mri/brainmask.mgz': No such file or directory
#--------------------------------------------
#@# Skull Stripping Fri Feb 19 19:11:39 UTC 2021
/mnt/vredemo/practice_with_data/skullstrip1_before/mri

 mri_watershed -T1 -h 1 T1.mgz brainmask.auto.mgz 


Mode:          T1 normalized volume
Mode:          Preflooding height manually specified

*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz

*************************WATERSHED**************************
Sorting...
      T1-weighted MRI image
      Count how many 110 voxels are present :  350210

      Find the largest 110-component...
             heap usage = 250940 Kbytes.
             current max segment has 173585 voxels
             removing small segments (less than 1 percent of maxarea).
             heap usage = 167492 Kbytes.
             removing small segments (less than 1 percent of maxarea).done
      And identify it as the main brain basin...done
      Main component: 173585 voxels
      first estimation of the COG coord: x=126 y=115 z=112 r=89
      first estimation of the main basin volume: 2981949 voxels
      global maximum in x=149, y=94, z=69, Imax=255
      CSF=17, WM_intensity=110, WM_VARIANCE=5
      WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
      preflooding height equal to 1 percent
done.
Analyze...

      main basin size=  989740 voxels, voxel volume =1.000 
                     = 989740 mmm3 = 989.740 cm3
done.
PostAnalyze...
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 194 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 47 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2545 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 29 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2714 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 15 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 231 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 13 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 141 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 298 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 86 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 17 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 62 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 26 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 17 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 7 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 219 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 15 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 23 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 18 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 15 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 20 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 45 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 27 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 20 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 18 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 10 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 52 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 226 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 42 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 965 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 76 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 184 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 19 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 42 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 23 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 26 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 29 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 10 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 173 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 41 voxels
      ambiguous basin, merged: at least 17 ambiguous voxels; size: 4729 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1136 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 554 voxels
      ambiguous basin, merged: at least 15 ambiguous voxels; size: 3366 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 10 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 29 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 153 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1419 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 13 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1528 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 27 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1533 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2537 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 498 voxels
      ambiguous basin, merged: at least 13 ambiguous voxels; size: 1738 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1281 voxels
      ambiguous basin, merged: at least 13 ambiguous voxels; size: 1804 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2199 voxels
      ambiguous basin, merged: at least 13 ambiguous voxels; size: 1872 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1450 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 15 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1344 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 577 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 130 voxels
      ambiguous basin, merged: at least 15 ambiguous voxels; size: 2750 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 237 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 833 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 507 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2525 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 19 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 13 ambiguous voxels; size: 1773 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 259 voxels
      ambiguous basin, merged: at least 13 ambiguous voxels; size: 1971 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 307 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 229 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 46 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 556 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 18 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 237 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 10 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 387 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 100 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 51 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 53 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 280 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 668 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 242 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 8 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 63 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 38 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 46 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 21 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 19 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1632 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 172 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 204 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 363 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 20 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 626 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 61 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 72 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 27 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 529 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1615 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 8 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 189 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1170 voxels
      ambiguous basin, merged: at least 13 ambiguous voxels; size: 2181 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 901 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 84 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 64 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 68 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 508 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 20 voxels
      ambiguous basin, merged: at least 20 ambiguous voxels; size: 7828 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 18 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 10 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 8 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 200 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 25 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 7 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 281 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1063 voxels
      ambiguous basin, merged: at least 13 ambiguous voxels; size: 1960 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 10 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 25 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1716 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 722 voxels
      ambiguous basin, merged: at least 13 ambiguous voxels; size: 1930 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 8 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 874 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 176 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 116 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 375 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 54 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 603 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 7 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 42 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 18 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 19 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 10 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 94 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 21 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 42 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 60 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 59 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 728 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 920 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 22 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1438 voxels
      ambiguous basin, merged: at least 15 ambiguous voxels; size: 3216 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1107 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 833 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 633 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 738 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1274 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 18 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 788 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 692 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 10 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 36 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2732 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 13 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 103 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 545 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 327 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 119 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 727 voxels
      ambiguous basin, merged: at least 15 ambiguous voxels; size: 2889 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1076 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1139 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2254 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 86 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 468 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 236 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 63 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 19 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 144 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 53 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2741 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 310 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1494 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 462 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 49 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1194 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 17 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 8 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1329 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 33 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 42 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 71 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1283 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 108 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 91 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 41 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 633 voxels
      ambiguous basin, merged: at least 13 ambiguous voxels; size: 2012 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 488 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 69 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 996 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 56 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 20 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 255 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 81 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 703 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 25 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 922 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 33 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 47 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 89 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 23 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1126 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 913 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 266 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 868 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 642 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 444 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 13 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 278 voxels
      ***** 264 basin(s) merged in 7 iteration(s)
      ***** 128123 voxel(s) added to the main basin
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 26 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 18 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 35 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 41 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 11 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 16 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 26 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 8 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 8 voxels
      ambiguous basin, non merged: 5 ambiguous voxels; size: 132 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 14 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 11 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 43 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 13 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 216 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 57 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
done.

****************TEMPLATE DEFORMATION****************

      second estimation of the COG coord: x=125,y=94, z=117, r=9469 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=25, CSF_MAX=63 , nb = 22554
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    63,      60,        59,   78
  after  analyzing :    51,      60,        60,   64
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...67 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.013
curvature mean = 63.906, std = 8.683

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 4.33, sigma = 6.39
      after  rotation: sse = 4.33, sigma = 6.39
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  5.11, its var is  7.79   
      before Erosion-Dilatation  2.59% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...39 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1388799 voxels, voxel volume = 1.000 mm3
           = 1388799 mmm3 = 1388.799 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    27.116560
mri_watershed stimesec    0.529931
mri_watershed ru_maxrss   350652
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   133247
mri_watershed ru_majflt   6
mri_watershed ru_nswap    0
mri_watershed ru_inblock  9168
mri_watershed ru_oublock  2120
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    116
mri_watershed ru_nivcsw   2305
mri_watershed done
@#@FSTIME  2021:02:19:19:11:39 mri_watershed N 5 e 28.12 S 0.56 U 27.14 P 98% M 350652 F 6 R 135630 W 0 c 2316 w 166 I 9168 O 2120 L 0.46 0.30 0.20
@#@FSLOADPOST 2021:02:19:19:12:07 mri_watershed N 5 0.64 0.36 0.22

 cp brainmask.auto.mgz brainmask.mgz 

#@# white curv lh Fri Feb 19 19:12:09 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
   Update not needed
#@# white area lh Fri Feb 19 19:12:09 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
   Update not needed
#@# pial curv lh Fri Feb 19 19:12:09 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
   Update not needed
#@# pial area lh Fri Feb 19 19:12:09 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
   Update not needed
#@# thickness lh Fri Feb 19 19:12:09 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness
   Update not needed
#@# area and vertex vol lh Fri Feb 19 19:12:09 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness
   Update not needed
#@# white curv rh Fri Feb 19 19:12:09 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
   Update not needed
#@# white area rh Fri Feb 19 19:12:09 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
   Update not needed
#@# pial curv rh Fri Feb 19 19:12:09 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
   Update not needed
#@# pial area rh Fri Feb 19 19:12:09 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
   Update not needed
#@# thickness rh Fri Feb 19 19:12:09 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness
   Update not needed
#@# area and vertex vol rh Fri Feb 19 19:12:09 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness
   Update not needed

Started at Fri Feb 19 19:11:38 UTC 2021 
Ended   at Fri Feb 19 19:12:09 UTC 2021
#@#%# recon-all-run-time-hours 0.009
recon-all -s skullstrip1_before finished without error at Fri Feb 19 19:12:10 UTC 2021



#New# invocation of recon-all 




Fri Feb 19 21:18:15 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before
setenv SUBJECTS_DIR /mnt/vredemo/practice_with_data
/mnt/vredemo/freesurfer/bin/recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid skullstrip1_before

subjid skullstrip1_before
setenv SUBJECTS_DIR /mnt/vredemo/practice_with_data
FREESURFER_HOME /mnt/vredemo/freesurfer
Actual FREESURFER_HOME /mnt/vredemo/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
Linux ivysaur-12.ldap.indocresearch.org 5.4.0-53-generic #59-Ubuntu SMP Wed Oct 21 09:38:44 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 65536 kbytes
maxproc      63380 
maxlocks     unlimited
maxsignal    63380 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           15Gi       3.3Gi       5.2Gi        60Mi       7.1Gi        11Gi
Swap:            0B          0B          0B

########################################
program versions used
7.1.1 (freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551)
7.1.1

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:15-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:15-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:15-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:15-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:15-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.1

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.1

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.1
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:18:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /mnt/vredemo/freesurfer/average
GCA RB_all_2020-01-02.gca
GCASkull RB_all_withskull_2020_01_02.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /mnt/vredemo/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################

 mv -f /mnt/vredemo/practice_with_data/skullstrip1_before/mri/brainmask.mgz /mnt/vredemo/practice_with_data/skullstrip1_before/trash 

#--------------------------------------------
#@# Skull Stripping Fri Feb 19 21:18:17 UTC 2021
/mnt/vredemo/practice_with_data/skullstrip1_before/mri

 mri_watershed -T1 -h 35 T1.mgz brainmask.auto.mgz 


Mode:          T1 normalized volume
Mode:          Preflooding height manually specified

*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz

*************************WATERSHED**************************
Sorting...
      T1-weighted MRI image
      Count how many 110 voxels are present :  350210

      Find the largest 110-component...
             heap usage = 251016 Kbytes.
             current max segment has 173585 voxels
             removing small segments (less than 1 percent of maxarea).
             heap usage = 167568 Kbytes.
             removing small segments (less than 1 percent of maxarea).done
      And identify it as the main brain basin...done
      Main component: 173585 voxels
      first estimation of the COG coord: x=126 y=115 z=112 r=89
      first estimation of the main basin volume: 2981949 voxels
      global maximum in x=149, y=94, z=69, Imax=255
      CSF=17, WM_intensity=110, WM_VARIANCE=5
      WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
      preflooding height equal to 35 percent
done.
Analyze...

      main basin size= 1757605 voxels, voxel volume =1.000 
                     = 1757605 mmm3 = 1757.605 cm3
done.
PostAnalyze...
      ***** 0 basin(s) merged in 1 iteration(s)
      ***** 0 voxel(s) added to the main basin
done.

****************TEMPLATE DEFORMATION****************

      second estimation of the COG coord: x=124,y=96, z=113, r=9955 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=54 , nb = 41868
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    54,      56,        58,   79
  after  analyzing :    54,      57,        58,   62
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...73 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.012
curvature mean = 69.961, std = 7.985

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 2.40, sigma = 3.79
      after  rotation: sse = 2.40, sigma = 3.79
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  2.42, its var is  3.05   
      before Erosion-Dilatation  0.07% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...49 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1769074 voxels, voxel volume = 1.000 mm3
           = 1769074 mmm3 = 1769.074 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    23.006949
mri_watershed stimesec    0.581590
mri_watershed ru_maxrss   352232
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   133644
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  408
mri_watershed ru_oublock  2768
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    84
mri_watershed ru_nivcsw   1106
mri_watershed done
@#@FSTIME  2021:02:19:21:18:17 mri_watershed N 5 e 23.98 S 0.62 U 23.03 P 98% M 352232 F 0 R 136014 W 0 c 1111 w 132 I 408 O 2768 L 0.20 0.34 0.52
@#@FSLOADPOST 2021:02:19:21:18:41 mri_watershed N 5 0.61 0.43 0.54

 cp brainmask.auto.mgz brainmask.mgz 

#@# white curv lh Fri Feb 19 21:18:42 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
   Update not needed
#@# white area lh Fri Feb 19 21:18:42 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
   Update not needed
#@# pial curv lh Fri Feb 19 21:18:42 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
   Update not needed
#@# pial area lh Fri Feb 19 21:18:42 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
   Update not needed
#@# thickness lh Fri Feb 19 21:18:42 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness
   Update not needed
#@# area and vertex vol lh Fri Feb 19 21:18:42 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness
   Update not needed
#@# white curv rh Fri Feb 19 21:18:42 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
   Update not needed
#@# white area rh Fri Feb 19 21:18:43 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
   Update not needed
#@# pial curv rh Fri Feb 19 21:18:43 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
   Update not needed
#@# pial area rh Fri Feb 19 21:18:43 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
   Update not needed
#@# thickness rh Fri Feb 19 21:18:43 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness
   Update not needed
#@# area and vertex vol rh Fri Feb 19 21:18:43 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness
   Update not needed

Started at Fri Feb 19 21:18:15 UTC 2021 
Ended   at Fri Feb 19 21:18:43 UTC 2021
#@#%# recon-all-run-time-hours 0.008
recon-all -s skullstrip1_before finished without error at Fri Feb 19 21:18:43 UTC 2021



#New# invocation of recon-all 




Fri Feb 19 21:23:16 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before
setenv SUBJECTS_DIR /mnt/vredemo/practice_with_data
/mnt/vredemo/freesurfer/bin/recon-all -skullstrip -wsthresh 1 -clean-bm -no-wsgcaatlas -subjid skullstrip1_before

subjid skullstrip1_before
setenv SUBJECTS_DIR /mnt/vredemo/practice_with_data
FREESURFER_HOME /mnt/vredemo/freesurfer
Actual FREESURFER_HOME /mnt/vredemo/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
Linux ivysaur-12.ldap.indocresearch.org 5.4.0-53-generic #59-Ubuntu SMP Wed Oct 21 09:38:44 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 65536 kbytes
maxproc      63380 
maxlocks     unlimited
maxsignal    63380 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           15Gi       7.7Gi       742Mi        70Mi       7.1Gi       7.4Gi
Swap:            0B          0B          0B

########################################
program versions used
7.1.1 (freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551)
7.1.1

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.1

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.1

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:16-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.1
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:23:17-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /mnt/vredemo/freesurfer/average
GCA RB_all_2020-01-02.gca
GCASkull RB_all_withskull_2020_01_02.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /mnt/vredemo/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################

 mv -f /mnt/vredemo/practice_with_data/skullstrip1_before/mri/brainmask.mgz /mnt/vredemo/practice_with_data/skullstrip1_before/trash 

#--------------------------------------------
#@# Skull Stripping Fri Feb 19 21:23:17 UTC 2021
/mnt/vredemo/practice_with_data/skullstrip1_before/mri

 mri_watershed -T1 -h 1 T1.mgz brainmask.auto.mgz 


Mode:          T1 normalized volume
Mode:          Preflooding height manually specified

*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz

*************************WATERSHED**************************
Sorting...
      T1-weighted MRI image
      Count how many 110 voxels are present :  350210

      Find the largest 110-component...
             heap usage = 250940 Kbytes.
             current max segment has 173585 voxels
             removing small segments (less than 1 percent of maxarea).
             heap usage = 167492 Kbytes.
             removing small segments (less than 1 percent of maxarea).done
      And identify it as the main brain basin...done
      Main component: 173585 voxels
      first estimation of the COG coord: x=126 y=115 z=112 r=89
      first estimation of the main basin volume: 2981949 voxels
      global maximum in x=149, y=94, z=69, Imax=255
      CSF=17, WM_intensity=110, WM_VARIANCE=5
      WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
      preflooding height equal to 1 percent
done.
Analyze...

      main basin size=  989740 voxels, voxel volume =1.000 
                     = 989740 mmm3 = 989.740 cm3
done.
PostAnalyze...
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 194 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 47 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2545 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 29 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2714 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 15 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 231 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 13 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 141 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 298 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 86 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 17 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 62 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 26 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 17 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 7 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 219 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 15 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 23 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 18 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 15 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 20 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 45 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
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      ambiguous basin, merged: at least 3 ambiguous voxels; size: 20 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 18 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 10 voxels
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      ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 226 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 42 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 965 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 76 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 184 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 19 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 42 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 23 voxels
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      ambiguous basin, merged: at least 4 ambiguous voxels; size: 29 voxels
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      ambiguous basin, merged: at least 17 ambiguous voxels; size: 4729 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1136 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 554 voxels
      ambiguous basin, merged: at least 15 ambiguous voxels; size: 3366 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 10 voxels
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      ambiguous basin, merged: at least 6 ambiguous voxels; size: 153 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1419 voxels
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      ambiguous basin, merged: at least 3 ambiguous voxels; size: 13 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1528 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 27 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1533 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2537 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 498 voxels
      ambiguous basin, merged: at least 13 ambiguous voxels; size: 1738 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1281 voxels
      ambiguous basin, merged: at least 13 ambiguous voxels; size: 1804 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2199 voxels
      ambiguous basin, merged: at least 13 ambiguous voxels; size: 1872 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1450 voxels
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      ambiguous basin, merged: at least 9 ambiguous voxels; size: 577 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 130 voxels
      ambiguous basin, merged: at least 15 ambiguous voxels; size: 2750 voxels
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      ambiguous basin, merged: at least 10 ambiguous voxels; size: 833 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 507 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2525 voxels
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      ambiguous basin, merged: at least 7 ambiguous voxels; size: 259 voxels
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      ambiguous basin, merged: at least 7 ambiguous voxels; size: 307 voxels
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      ambiguous basin, merged: at least 5 ambiguous voxels; size: 100 voxels
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      ambiguous basin, merged: at least 6 ambiguous voxels; size: 172 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 204 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 363 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 20 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 626 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 61 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 72 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 27 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 529 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1615 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 8 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 189 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1170 voxels
      ambiguous basin, merged: at least 13 ambiguous voxels; size: 2181 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 901 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 84 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 64 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 68 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 508 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 20 voxels
      ambiguous basin, merged: at least 20 ambiguous voxels; size: 7828 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 18 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 10 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 8 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 200 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 25 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 7 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 281 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1063 voxels
      ambiguous basin, merged: at least 13 ambiguous voxels; size: 1960 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 10 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 25 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1716 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 722 voxels
      ambiguous basin, merged: at least 13 ambiguous voxels; size: 1930 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
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      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 8 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 874 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 176 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 116 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 375 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 54 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 603 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 7 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 42 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 18 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 19 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 10 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 94 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 21 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 42 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 60 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 59 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 728 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 920 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 22 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1438 voxels
      ambiguous basin, merged: at least 15 ambiguous voxels; size: 3216 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1107 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 833 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 633 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 738 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1274 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 18 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 788 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 692 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 10 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 36 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2732 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 13 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 103 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 545 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 327 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 119 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 727 voxels
      ambiguous basin, merged: at least 15 ambiguous voxels; size: 2889 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1076 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1139 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2254 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 86 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 468 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 236 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 63 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 19 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 144 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 53 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2741 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 310 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 12 ambiguous voxels; size: 1494 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 462 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 49 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1194 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 17 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 8 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1329 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 33 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 42 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 71 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1283 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 108 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 91 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 41 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 633 voxels
      ambiguous basin, merged: at least 13 ambiguous voxels; size: 2012 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 488 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 69 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 996 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 56 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 20 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 255 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 81 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 703 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 25 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 922 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 33 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 47 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 89 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 23 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1126 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 913 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 266 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 868 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 642 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 444 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 13 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 278 voxels
      ***** 264 basin(s) merged in 7 iteration(s)
      ***** 128123 voxel(s) added to the main basin
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 12 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 8 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 13 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 6 ambiguous voxels; size: 1545 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 8 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 14 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 20 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 8 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 57 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
done.

****************TEMPLATE DEFORMATION****************

      second estimation of the COG coord: x=125,y=94, z=117, r=9469 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=25, CSF_MAX=63 , nb = 22554
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    63,      60,        59,   78
  after  analyzing :    51,      60,        60,   64
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...67 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.013
curvature mean = 63.906, std = 8.683

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 4.33, sigma = 6.39
      after  rotation: sse = 4.33, sigma = 6.39
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  5.11, its var is  7.79   
      before Erosion-Dilatation  2.59% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...39 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1388799 voxels, voxel volume = 1.000 mm3
           = 1388799 mmm3 = 1388.799 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    26.761217
mri_watershed stimesec    0.540338
mri_watershed ru_maxrss   350672
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   133245
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  2120
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    102
mri_watershed ru_nivcsw   831
mri_watershed done
@#@FSTIME  2021:02:19:21:23:17 mri_watershed N 5 e 27.55 S 0.57 U 26.78 P 99% M 350672 F 0 R 135622 W 0 c 840 w 150 I 0 O 2120 L 0.89 0.49 0.53
@#@FSLOADPOST 2021:02:19:21:23:45 mri_watershed N 5 0.93 0.54 0.55

 cp brainmask.auto.mgz brainmask.mgz 

#@# white curv lh Fri Feb 19 21:23:46 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
   Update not needed
#@# white area lh Fri Feb 19 21:23:46 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
   Update not needed
#@# pial curv lh Fri Feb 19 21:23:46 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
   Update not needed
#@# pial area lh Fri Feb 19 21:23:46 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
   Update not needed
#@# thickness lh Fri Feb 19 21:23:46 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness
   Update not needed
#@# area and vertex vol lh Fri Feb 19 21:23:46 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness
   Update not needed
#@# white curv rh Fri Feb 19 21:23:47 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
   Update not needed
#@# white area rh Fri Feb 19 21:23:47 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
   Update not needed
#@# pial curv rh Fri Feb 19 21:23:47 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
   Update not needed
#@# pial area rh Fri Feb 19 21:23:47 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
   Update not needed
#@# thickness rh Fri Feb 19 21:23:47 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness
   Update not needed
#@# area and vertex vol rh Fri Feb 19 21:23:47 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness
   Update not needed

Started at Fri Feb 19 21:23:15 UTC 2021 
Ended   at Fri Feb 19 21:23:47 UTC 2021
#@#%# recon-all-run-time-hours 0.009
recon-all -s skullstrip1_before finished without error at Fri Feb 19 21:23:47 UTC 2021



#New# invocation of recon-all 




Fri Feb 19 21:51:31 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before
setenv SUBJECTS_DIR /mnt/vredemo/practice_with_data
/mnt/vredemo/freesurfer/bin/recon-all -skullstrip -wsthresh 1 -clean-bm -no-wsgcaatlas -subjid skullstrip1_before

subjid skullstrip1_before
setenv SUBJECTS_DIR /mnt/vredemo/practice_with_data
FREESURFER_HOME /mnt/vredemo/freesurfer
Actual FREESURFER_HOME /mnt/vredemo/freesurfer
build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
Linux ivysaur-12.ldap.indocresearch.org 5.4.0-53-generic #59-Ubuntu SMP Wed Oct 21 09:38:44 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 65536 kbytes
maxproc      63380 
maxlocks     unlimited
maxsignal    63380 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:           15Gi       4.9Gi       1.3Gi        72Mi       9.4Gi        10Gi
Swap:            0B          0B          0B

########################################
program versions used
7.1.1 (freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551)
7.1.1

ProgramName: lta_convert  ProgramArguments: lta_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_and  ProgramArguments: mri_and -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_annotation2label  ProgramArguments: mri_annotation2label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg  ProgramArguments: mri_aparc2aseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg  ProgramArguments: mri_surf2volseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_binarize  ProgramArguments: mri_binarize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_label  ProgramArguments: mri_ca_label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize  ProgramArguments: mri_ca_normalize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_ca_register  ProgramArguments: mri_ca_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_cc  ProgramArguments: mri_cc -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap  ProgramArguments: mri_compute_overlap -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap  ProgramArguments: mri_compute_seg_overlap -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concat  ProgramArguments: mri_concat -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta  ProgramArguments: mri_concatenate_lta -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_diff  ProgramArguments: mri_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg  ProgramArguments: mri_edit_wm_with_aseg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_em_register  ProgramArguments: mri_em_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fill  ProgramArguments: mri_fill -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations  ProgramArguments: mri_fuse_segmentations -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_fwhm  ProgramArguments: mri_fwhm -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_gcut  ProgramArguments: mri_gcut -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_info  ProgramArguments: mri_info -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2label  ProgramArguments: mri_label2label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_label2vol  ProgramArguments: mri_label2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood  ProgramArguments: mri_log_likelihood -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_mask  ProgramArguments: mri_mask -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply  ProgramArguments: mri_matrix_multiply -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize  ProgramArguments: mri_normalize -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2  ProgramArguments: mri_normalize_tp2 -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_or  ProgramArguments: mri_or -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities  ProgramArguments: mri_relabel_hypointensities -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos  ProgramArguments: mri_relabel_nonwm_hypos -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_remove_neck  ProgramArguments: mri_remove_neck -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.1

ProgramName: mri_robust_register  ProgramArguments: mri_robust_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
7.1.1

ProgramName: mri_robust_template  ProgramArguments: mri_robust_template -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats  ProgramArguments: mris_anatomical_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_ca_label  ProgramArguments: mris_ca_label -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_calc  ProgramArguments: mris_calc -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_convert  ProgramArguments: mris_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature  ProgramArguments: mris_curvature -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats  ProgramArguments: mris_curvature_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_diff  ProgramArguments: mris_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation  ProgramArguments: mris_divide_parcellation -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segment  ProgramArguments: mri_segment -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_segstats  ProgramArguments: mri_segstats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_euler_number  ProgramArguments: mris_euler_number -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_fix_topology  ProgramArguments: mris_fix_topology -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_jacobian  ProgramArguments: mris_jacobian -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_label2annot  ProgramArguments: mris_label2annot -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_left_right_register  ProgramArguments: mris_left_right_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_place_surface  ProgramArguments: mris_place_surface -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mrisp_paint  ProgramArguments: mrisp_paint -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_register  ProgramArguments: mris_register -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_smooth  ProgramArguments: mris_smooth -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_sphere  ProgramArguments: mris_sphere -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_surface_stats  ProgramArguments: mris_surface_stats -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_stats2seg  ProgramArguments: mri_stats2seg -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:31-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness  ProgramArguments: mris_thickness -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff  ProgramArguments: mris_thickness_diff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer  ProgramArguments: mris_topo_fixer -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2surf  ProgramArguments: mri_surf2surf -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surf2vol  ProgramArguments: mri_surf2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_surfcluster  ProgramArguments: mri_surfcluster -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mris_volmask  ProgramArguments: mris_volmask -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_tessellate  ProgramArguments: mri_tessellate -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_voldiff  ProgramArguments: mri_voldiff -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: mri_watershed  ProgramArguments: mri_watershed -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
ProgramName: tkregister2  ProgramArguments: tkregister2_cmdl -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.1.1
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: mri_convert -all-info  ProgramVersion: 7.1.1  TimeStamp: 2021/02/19-21:51:32-GMT  BuildTime: Jul 23 2020 11:55:54  BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551  User: sliang  Machine: ivysaur-12.ldap.indocresearch.org  Platform: Linux  PlatformVersion: 5.4.0-53-generic  CompilerName: GCC  CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /mnt/vredemo/freesurfer/average
GCA RB_all_2020-01-02.gca
GCASkull RB_all_withskull_2020_01_02.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /mnt/vredemo/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################

 mv -f /mnt/vredemo/practice_with_data/skullstrip1_before/mri/brainmask.mgz /mnt/vredemo/practice_with_data/skullstrip1_before/trash 

#--------------------------------------------
#@# Skull Stripping Fri Feb 19 21:51:32 UTC 2021
/mnt/vredemo/practice_with_data/skullstrip1_before/mri

 mri_watershed -T1 -h 1 T1.mgz brainmask.auto.mgz 


Mode:          T1 normalized volume
Mode:          Preflooding height manually specified

*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz

*************************WATERSHED**************************
Sorting...
      T1-weighted MRI image
      Count how many 110 voxels are present :  350210

      Find the largest 110-component...
             heap usage = 250940 Kbytes.
             current max segment has 173585 voxels
             removing small segments (less than 1 percent of maxarea).
             heap usage = 167492 Kbytes.
             removing small segments (less than 1 percent of maxarea).done
      And identify it as the main brain basin...done
      Main component: 173585 voxels
      first estimation of the COG coord: x=126 y=115 z=112 r=89
      first estimation of the main basin volume: 2981949 voxels
      global maximum in x=149, y=94, z=69, Imax=255
      CSF=17, WM_intensity=110, WM_VARIANCE=5
      WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
      preflooding height equal to 1 percent
done.
Analyze...

      main basin size=  989740 voxels, voxel volume =1.000 
                     = 989740 mmm3 = 989.740 cm3
done.
PostAnalyze...
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 194 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 47 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2545 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 29 voxels
      ambiguous basin, merged: at least 14 ambiguous voxels; size: 2714 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 15 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 231 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 13 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 141 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 298 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 86 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 17 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 62 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 26 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 17 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 7 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 219 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 15 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 23 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 18 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 15 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 20 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 45 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 12 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 27 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 20 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 18 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 10 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 52 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 226 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 42 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 965 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 76 voxels
      ambiguous basin, merged: at least 6 ambiguous voxels; size: 184 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 19 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 42 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 23 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 26 voxels
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      ambiguous basin, merged: at least 7 ambiguous voxels; size: 310 voxels
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      ambiguous basin, merged: at least 3 ambiguous voxels; size: 17 voxels
      ambiguous basin, merged: at least 2 ambiguous voxels; size: 8 voxels
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      ambiguous basin, merged: at least 4 ambiguous voxels; size: 33 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 42 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 71 voxels
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      ambiguous basin, merged: at least 5 ambiguous voxels; size: 108 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 91 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 9 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 41 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 633 voxels
      ambiguous basin, merged: at least 13 ambiguous voxels; size: 2012 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 488 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 69 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 996 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 56 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 20 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 255 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 81 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 703 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 16 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 25 voxels
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      ambiguous basin, merged: at least 4 ambiguous voxels; size: 33 voxels
      ambiguous basin, merged: at least 4 ambiguous voxels; size: 47 voxels
      ambiguous basin, merged: at least 5 ambiguous voxels; size: 89 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 23 voxels
      ambiguous basin, merged: at least 11 ambiguous voxels; size: 1126 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 913 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 266 voxels
      ambiguous basin, merged: at least 10 ambiguous voxels; size: 868 voxels
      ambiguous basin, merged: at least 9 ambiguous voxels; size: 642 voxels
      ambiguous basin, merged: at least 8 ambiguous voxels; size: 444 voxels
      ambiguous basin, merged: at least 3 ambiguous voxels; size: 13 voxels
      ambiguous basin, merged: at least 7 ambiguous voxels; size: 278 voxels
      ***** 264 basin(s) merged in 7 iteration(s)
      ***** 128123 voxel(s) added to the main basin
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 12 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 8 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
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      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 10 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 22 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 36 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 11 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 162 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 16 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 6 ambiguous voxels; size: 599 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 8 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 25 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 11 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 53 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 64 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 10 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 26 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 18 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 35 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 41 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 11 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 16 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 26 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 8 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 8 voxels
      ambiguous basin, non merged: 5 ambiguous voxels; size: 132 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 6 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 7 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 14 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 11 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 43 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 13 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 9 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 216 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 2 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 5 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 57 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels
      ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels
done.

****************TEMPLATE DEFORMATION****************

      second estimation of the COG coord: x=125,y=94, z=117, r=9469 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=25, CSF_MAX=63 , nb = 22554
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    63,      60,        59,   78
  after  analyzing :    51,      60,        60,   64
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...67 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.013
curvature mean = 63.906, std = 8.683

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 4.33, sigma = 6.39
      after  rotation: sse = 4.33, sigma = 6.39
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  5.11, its var is  7.79   
      before Erosion-Dilatation  2.59% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...39 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1388799 voxels, voxel volume = 1.000 mm3
           = 1388799 mmm3 = 1388.799 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    23.731090
mri_watershed stimesec    0.426881
mri_watershed ru_maxrss   350688
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   133242
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  2120
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    102
mri_watershed ru_nivcsw   1008
mri_watershed done
@#@FSTIME  2021:02:19:21:51:32 mri_watershed N 5 e 24.42 S 0.46 U 23.75 P 99% M 350688 F 0 R 135583 W 0 c 1016 w 153 I 0 O 2120 L 0.19 0.12 0.23
@#@FSLOADPOST 2021:02:19:21:51:57 mri_watershed N 5 0.46 0.20 0.25

 cp brainmask.auto.mgz brainmask.mgz 

#@# white curv lh Fri Feb 19 21:51:58 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
   Update not needed
#@# white area lh Fri Feb 19 21:51:58 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
   Update not needed
#@# pial curv lh Fri Feb 19 21:51:58 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
   Update not needed
#@# pial area lh Fri Feb 19 21:51:58 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
   Update not needed
#@# thickness lh Fri Feb 19 21:51:58 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness
   Update not needed
#@# area and vertex vol lh Fri Feb 19 21:51:58 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness
   Update not needed
#@# white curv rh Fri Feb 19 21:51:58 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
   Update not needed
#@# white area rh Fri Feb 19 21:51:58 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
   Update not needed
#@# pial curv rh Fri Feb 19 21:51:58 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
   Update not needed
#@# pial area rh Fri Feb 19 21:51:58 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
   Update not needed
#@# thickness rh Fri Feb 19 21:51:58 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness
   Update not needed
#@# area and vertex vol rh Fri Feb 19 21:51:58 UTC 2021
cd /mnt/vredemo/practice_with_data/skullstrip1_before/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness
   Update not needed

Started at Fri Feb 19 21:51:30 UTC 2021 
Ended   at Fri Feb 19 21:51:58 UTC 2021
#@#%# recon-all-run-time-hours 0.008
recon-all -s skullstrip1_before finished without error at Fri Feb 19 21:51:59 UTC 2021
